callset ID	vcf	reference	variant type	SNP or INDEL	chr	chrwithprefix	GRCh37_POS	GRCh38_POS	Distance from previous position	Is this a putative FP, FN or genotype error (FP_FN) in your calls?	ref	alt	format_field	truth_gt or for "common" truth_gt when comparing to Roche callset	query_gt or for "common" query_gt when comparing to Roche callset	Is this variant and all variants and genotypes in the surrounding region (e.g., in the same tandem repeat) correct in the benchmark? (yes, no, or unsure)	Is this variant and all variants and genotypes in the surrounding region (e.g., in the same tandem repeat) correct in the query callset? (yes, no, or unsure)	Notes (required if answer is no or unsure for the benchmark)	JZ- Is this variant and all variants and genotypes in the surrounding region (e.g., in the same tandem repeat) correct in the benchmark? (yes, no, or unsure)	JZ - Is this variant and all variants and genotypes in the surrounding region (e.g., in the same tandem repeat) correct in the query callset? (yes, no, or unsure)	JZ - Notes	JW- Is this variant and all variants and genotypes in the surrounding region (e.g., in the same tandem repeat) correct in the benchmark? (yes, no, or unsure)	JW - Is this variant and all variants and genotypes in the surrounding region (e.g., in the same tandem repeat) correct in the query callset? (yes, no, or unsure)	JW - Notes	JM- Is this variant and all variants and genotypes in the surrounding region (e.g., in the same tandem repeat) correct in the benchmark? (yes, no, or unsure)	JM - Is this variant and all variants and genotypes in the surrounding region (e.g., in the same tandem repeat) correct in the query callset? (yes, no, or unsure)	JM - Notes	SM- Is this variant and all variants and genotypes in the surrounding region (e.g., in the same tandem repeat) correct in the benchmark? (yes, no, or unsure)	SM - Is this variant and all variants and genotypes in the surrounding region (e.g., in the same tandem repeat) correct in the query callset? (yes, no, or unsure)	SM - Notes	LH- Is this variant and all variants and genotypes in the surrounding region (e.g., in the same tandem repeat) correct in the benchmark? (yes, no, or unsure)	LH - Is this variant and all variants and genotypes in the surrounding region (e.g., in the same tandem repeat) correct in the query callset? (yes, no, or unsure)	LH - Notes	truth_gt when comparing to PacBio_gatk4 callset	query_gt when comparing to PacBio_gatk4 callset	truth_gt when comparing to NYGC callset	query_gt when comparing to NYGC callset	truth_gt when comparing to NCBI callset	query_gt when comparing to NCBI callset	truth_gt when comparing to ITER callset	query_gt when comparing to ITER callset	truth_gt when comparing to DNAnexus callset	query_gt when comparing to DNAnexus callset	truth_gt when comparing to CMH_DRAGEN_3.6.3 callset	query_gt when comparing to CMH_DRAGEN_3.6.3 callset	truth_gt when comparing to BCM-HGSC_xAtlas callset	query_gt when comparing to BCM-HGSC_xAtlas callset		GRCh37_POS
Common		GRCh37			1	chr1	956227	1020847	0	FP_FN	C	CGGG,CGGGG	GT:BD:BK:QQ:BI:BVT:BLT	2|2:FN:am:.:i1_5:INDEL:homalt	2/1:FP:am:100:i1_5:INDEL:hetalt	CommonFP_FN			no	yes	likely benchmark error due to noisy HiFi reads and clean illumina reads for 3bp ins in long homopolymer													2|2:FN:am:.:i1_5:INDEL:homalt	2/1:FP:am:782.73:i1_5:INDEL:hetalt	2|2:FN:lm:.:i1_5:INDEL:homalt	1/1:FP:lm:546.73:i1_5:INDEL:homalt	2|2:TP:gm:30:i1_5:INDEL:homalt	2/2:TP:gm:30:i1_5:INDEL:homalt	2|2:FN:.:.:i1_5:INDEL:homalt	.:.:.:0:.:NOCALL:nocall	2|2:FN:lm:.:i1_5:INDEL:homalt	1/1:FP:lm:0:i1_5:INDEL:homalt	2|2:FN:lm:.:i1_5:INDEL:homalt	1/1:FP:lm:109.41:i1_5:INDEL:homalt	2|2:FN:lm:.:i1_5:INDEL:homalt	1/1:FP:lm:10:i1_5:INDEL:homalt	1:956227	1020847
Common		GRCh38			1	chr1	956227	1020847	14322	FP_FN	C	CGGG,CGGGG	GT:BD:BK:QQ:BI:BVT:BLT	2|2:FN:lm:.:i1_5:INDEL:homalt	1/1:FP:lm:100:i1_5:INDEL:homalt	CommonFP_FN			no	yes	likely benchmark error due to noisy HiFi reads and clean illumina reads for 3bp ins in long homopolymer				no	yes	homopolymer. Coverage is lower than expected for all third gen and not seeing HP separation. ILMN mostly support 3bp INS or with a few SNP+3bp INS.							2|2:FN:am:.:i1_5:INDEL:homalt	2/1:FP:am:782.73:i1_5:INDEL:hetalt	2|2:FN:lm:.:i1_5:INDEL:homalt	1/1:FP:lm:681.73:i1_5:INDEL:homalt	2|2:TP:gm:30:i1_5:INDEL:homalt	2/2:TP:gm:30:i1_5:INDEL:homalt	2|2:FN:.:.:i1_5:INDEL:homalt	.:.:.:0:.:NOCALL:nocall	2|2:FN:lm:.:i1_5:INDEL:homalt	1/1:FP:lm:0:i1_5:INDEL:homalt	2|2:FN:lm:.:i1_5:INDEL:homalt	1/1:FP:lm:109.43:i1_5:INDEL:homalt	2|2:FN:lm:.:i1_5:INDEL:homalt	1/1:FP:lm:10:i1_5:INDEL:homalt		956227
Roche	RN_HG002_Illumina_PacBio_Oxford_GRCh37.vcf.gz	GRCh37	small-variants	INDEL	1	chr1	970549	1035169	14562	FP	TG	T	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	1/1:100:FP:.:d1_5:INDEL:homalt 	unsure		seems suspicious, in ILM there are not many reads that span the hp region and support the reference, in PB there is some evidence for the variant	unsure	unsure	all techs noisy in G homopolymer																											1:970549	1035169
DNAnexus	hs37d5_HG002_WGS_union.vcf.gz	GRCh37	small-variants	INDEL	1	chr1	985111	1049731	0	FN	C	CG	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	unsure	no	Compiled halotype 1 seemed to report this insertion. However, all other tracks don't seem to support this insertion. 	no	yes	likely benchmark error due to strangely noisy HiFi reads in 4bp homopolymer																											1:985111	1049731
Common		GRCh37			1	chr1	985111	1049731	0	FN	C	CG	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no	yes	likely benchmark error due to strangely noisy HiFi reads in 4bp homopolymer													1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1:985111	1049731
CMH_DRAGEN_3.6.3	NA24385.hard-filtered.vcf.gz	GRCh38	small-variants	INDEL	1	chr1	985111	1049731	0	FN	C	CG	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	unsure	unsure	Not supported by ILMN sets. Although evidenced in PacBio, PacBio reads are inconsistent among haplotags, and inconsistent among reads spanning the phased variant at chr1:1049886	no	yes	likely benchmark error due to strangely noisy HiFi reads in 4bp homopolymer				no	yes	no evidence of variant in ILMN or 10X. However 10X does not appear to be HP seperated. Minimal evidence in HiFi and not consistent with haplotypes.																						985111
Common		GRCh38			1	chr1	985111	1049731	5154805	FN	C	CG	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no	yes	likely benchmark error due to strangely noisy HiFi reads in 4bp homopolymer													1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0		985111
BCM-HGSC_xAtlas	HG002.GRCh38.60x.1_merged.vcf.gz	GRCh38	small-variants	INDEL	1	chr1	6264596	6204536	231946	FN	CA	C,CAA	GT:BD:BK:BI:BVT:BLT:QQ	2|1:FN:am:d1_5,i1_5:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:7 	Yes	No								skip																								6264596
NCBI	HG002_grch37_dipcall.vcf.gz	GRCh37	small-variants	INDEL	1	chr1	6496542	6436482	0	FP_FN	C	CTTAT	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:30:i1_5:INDEL:het	no	yes	evidence for HET INS here; segdup region	no	yes	likely benchmark error in TR due to highly homozygous region																											1:6496542	6436482
Common		GRCh37			1	chr1	6496542	6436482	0	FP_FN	C	CTTAT	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:100:i1_5:INDEL:het	CommonFP_FN			no	yes	likely benchmark error in TR due to highly homozygous region													1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:761.73:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:681.73:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:30:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:375.64:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:0:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:50:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:15:i1_5:INDEL:het	1:6496542	6436482
Common		GRCh38			1	chr1	6496542	6436482	17448786	FP_FN	C	CTTAT	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:100:i1_5:INDEL:het	CommonFP_FN			no	yes	likely benchmark error in TR due to highly homozygous region													1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:761.73:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:682.73:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:30:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:555.64:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:0:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:50:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:15:i1_5:INDEL:het		6496542
ITER	ITERteam_small-variation_GRCh38_ILMN-PB-ONT.vcf.gz	GRCh38	small-variants	INDEL	1	chr1	24211758	23885268	5477	FP	T	TA	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	1/1:4.6:FP:lm:i1_5:INDEL:homalt	Yes	No	No support in all technologies. There is another SNP in a previous position (2nt) detected by both truth and query.							skip																								24211758
PacBio_gatk4	gatk4hc_HG002_15kb_20kb_53X_SequelII.vcf.gz	GRCh38	small-variants	INDEL	1	chr1	24217235	23890745	3896	FP_FN	CA	C	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:371.74:d1_5:INDEL:het	yes	no								skip																								24217235
Common		GRCh37			1	chr1	24221131	23894641	39039	FP_FN	T	TAA,TAAA,TAAAAA	GT:BD:BK:BI:QQ:BVT:BLT	2|1:TP:gm:i1_5:100:INDEL:hetalt	2/1:TP:gm:i1_5:100:INDEL:hetalt	CommonFP_FN			yes	no	CNR2 is annotated on GRCh37 to include a large region downstream that has an erroneous extra unplaced contig on chr1 only in GRCh37 (chr1_gl000191_random) that interferes with mapping to a 106 kb region that includes part of CNR2 as well as other genes PNRC2 and SRSF10 not included in our medical gene list													2|1:FN:lm:i1_5:.:INDEL:hetalt	.:.:.:.:0:NOCALL:nocall	2|1:FN:am:i1_5:.:INDEL:hetalt	2/2:FP:am:i1_5:671.73:INDEL:homalt	2|1:FN:am:i1_5:.:INDEL:hetalt	2/2:FP:am:i1_5:30:INDEL:homalt	2|1:FN:am:i1_5:.:INDEL:hetalt	1/1:FP:am:i1_5:498.13:INDEL:homalt	2|1:FN:lm:i1_5:.:INDEL:hetalt	3/3:FP:lm:i1_5:0:INDEL:homalt	2|1:TP:gm:i1_5:137.51:INDEL:hetalt	2/1:TP:gm:i1_5:137.51:INDEL:hetalt	2|1:FN:am:i1_5:.:INDEL:hetalt	1/1:FP:am:i1_5:3:INDEL:homalt	1:24221131	23894641
NYGC	HG-002-2x250-b37.recalibrated.haplotypeCalls.vcf.gz	GRCh37	small-variants	SNP	1	chr1	24260170	23933680	46	FN	C	T	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0 	yes	no		yes	no	CNR2 is annotated on GRCh37 to include a large region downstream that has an erroneous extra unplaced contig on chr1 only in GRCh37 (chr1_gl000191_random) that interferes with mapping to a 106 kb region that includes part of CNR2 as well as other genes PNRC2 and SRSF10 not included in our medical gene list																											1:24260170	23933680
Common		GRCh37			1	chr1	24260216	23933726	1517	FN	C	T	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:lm:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	CNR2 is annotated on GRCh37 to include a large region downstream that has an erroneous extra unplaced contig on chr1 only in GRCh37 (chr1_gl000191_random) that interferes with mapping to a 106 kb region that includes part of CNR2 as well as other genes PNRC2 and SRSF10 not included in our medical gene list													0|1:TP:gm:ti:SNP:het:683.77	0/1:TP:gm:ti:SNP:het:683.77	0|1:FN:lm:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:TP:gm:ti:SNP:het:30	0/1:TP:gm:ti:SNP:het:30	0|1:TP:gm:ti:SNP:het:376.28	0/1:TP:gm:ti:SNP:het:376.28	0|1:FN:lm:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1:24260216	23933726
NYGC	HG-002-2x250-b37.recalibrated.haplotypeCalls.vcf.gz	GRCh37	small-variants	SNP	1	chr1	24261733	23935243	3570	FN	G	C	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0 	yes	no		yes	no	CNR2 is annotated on GRCh37 to include a large region downstream that has an erroneous extra unplaced contig on chr1 only in GRCh37 (chr1_gl000191_random) that interferes with mapping to a 106 kb region that includes part of CNR2 as well as other genes PNRC2 and SRSF10 not included in our medical gene list																											1:24261733	23935243
Common		GRCh37			1	chr1	24265303	23938813	1720	FN	AAAG	A	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:.:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	CNR2 is annotated on GRCh37 to include a large region downstream that has an erroneous extra unplaced contig on chr1 only in GRCh37 (chr1_gl000191_random) that interferes with mapping to a 106 kb region that includes part of CNR2 as well as other genes PNRC2 and SRSF10 not included in our medical gene list													1|1:TP:gm:d1_5:INDEL:homalt:256.73	1/1:TP:gm:d1_5:INDEL:homalt:256.73	1|1:FN:.:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:d1_5:INDEL:homalt:30	1/1:TP:gm:d1_5:INDEL:homalt:30	1|1:FN:.:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1:24265303	23938813
ITER	ITERteam_small-variation_GRCh37_ILMN-PB-ONT.vcf.gz	GRCh37	small-variants	INDEL	1	chr1	24267023	23940533	0	FN	C	CT	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	Yes	No		yes	no	CNR2 is annotated on GRCh37 to include a large region downstream that has an erroneous extra unplaced contig on chr1 only in GRCh37 (chr1_gl000191_random) that interferes with mapping to a 106 kb region that includes part of CNR2 as well as other genes PNRC2 and SRSF10 not included in our medical gene list																											1:24267023	23940533
Common		GRCh37			1	chr1	24267023	23940533	1910	FN	C	CT	GT:BD:BK:QQ:BI:BVT:BLT	0|1:TP:gm:7.4682:i1_5:INDEL:het	0/1:TP:gm:7.4682:i1_5:INDEL:het	CommonFN			yes	no	CNR2 is annotated on GRCh37 to include a large region downstream that has an erroneous extra unplaced contig on chr1 only in GRCh37 (chr1_gl000191_random) that interferes with mapping to a 106 kb region that includes part of CNR2 as well as other genes PNRC2 and SRSF10 not included in our medical gene list													0|1:TP:gm:20.77:i1_5:INDEL:het	0/1:TP:gm:20.77:i1_5:INDEL:het	0|1:FN:.:.:i1_5:INDEL:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:.:.:i1_5:INDEL:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:.:.:i1_5:INDEL:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:.:.:i1_5:INDEL:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:.:.:i1_5:INDEL:het	.:.:.:0:.:NOCALL:nocall	0|1:TP:gm:3:i1_5:INDEL:het	0/1:TP:gm:3:i1_5:INDEL:het	1:24267023	23940533
Common		GRCh37			1	chr1	24268933	23942443	1498	FN	C	T	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	CNR2 is annotated on GRCh37 to include a large region downstream that has an erroneous extra unplaced contig on chr1 only in GRCh37 (chr1_gl000191_random) that interferes with mapping to a 106 kb region that includes part of CNR2 as well as other genes PNRC2 and SRSF10 not included in our medical gene list													0|1:TP:gm:ti:SNP:het:197.78	0/1:TP:gm:ti:SNP:het:197.78	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:TP:gm:ti:SNP:het:30	0/1:TP:gm:ti:SNP:het:30	0|1:TP:gm:ti:SNP:het:32.5	0/1:TP:gm:ti:SNP:het:32.5	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1:24268933	23942443
Common		GRCh37			1	chr1	24270431	23943941	3066	FN	A	AC	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	CNR2 is annotated on GRCh37 to include a large region downstream that has an erroneous extra unplaced contig on chr1 only in GRCh37 (chr1_gl000191_random) that interferes with mapping to a 106 kb region that includes part of CNR2 as well as other genes PNRC2 and SRSF10 not included in our medical gene list													0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:TP:gm:i1_5:INDEL:het:30	0/1:TP:gm:i1_5:INDEL:het:30	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1:24270431	23943941
Roche	RN_HG002_Illumina_PacBio_Oxford_GRCh37.vcf.gz	GRCh37	small-variants	INDEL	1	chr1	24273497	23947007	384	FP	TC	T	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:11.4065:FP:.:d1_5:INDEL:het 	yes	no		yes	no	CNR2 is annotated on GRCh37 to include a large region downstream that has an erroneous extra unplaced contig on chr1 only in GRCh37 (chr1_gl000191_random) that interferes with mapping to a 106 kb region that includes part of CNR2 as well as other genes PNRC2 and SRSF10 not included in our medical gene list																											1:24273497	23947007
Common		GRCh37			1	chr1	24273881	23947391	412	FN	A	AT	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	CNR2 is annotated on GRCh37 to include a large region downstream that has an erroneous extra unplaced contig on chr1 only in GRCh37 (chr1_gl000191_random) that interferes with mapping to a 106 kb region that includes part of CNR2 as well as other genes PNRC2 and SRSF10 not included in our medical gene list													0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:TP:gm:i1_5:INDEL:het:30	0/1:TP:gm:i1_5:INDEL:het:30	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1:24273881	23947391
Common		GRCh37			1	chr1	24274293	23947803	855	FN	T	TTTATTATTA	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:.:i6_15:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	CNR2 is annotated on GRCh37 to include a large region downstream that has an erroneous extra unplaced contig on chr1 only in GRCh37 (chr1_gl000191_random) that interferes with mapping to a 106 kb region that includes part of CNR2 as well as other genes PNRC2 and SRSF10 not included in our medical gene list													1|1:FN:.:i6_15:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:i6_15:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:i6_15:INDEL:homalt:30	1/1:TP:gm:i6_15:INDEL:homalt:30	1|1:TP:gm:i6_15:INDEL:homalt:51.8	1/1:TP:gm:i6_15:INDEL:homalt:51.8	1|1:FN:.:i6_15:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:i6_15:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:i6_15:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1:24274293	23947803
Common		GRCh37			1	chr1	24275148	23948658	285	FN	CA	C	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	CNR2 is annotated on GRCh37 to include a large region downstream that has an erroneous extra unplaced contig on chr1 only in GRCh37 (chr1_gl000191_random) that interferes with mapping to a 106 kb region that includes part of CNR2 as well as other genes PNRC2 and SRSF10 not included in our medical gene list													0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:TP:gm:d1_5:INDEL:het:30	0/1:TP:gm:d1_5:INDEL:het:30	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1:24275148	23948658
Common		GRCh37			1	chr1	24275433	23948943	779	FN	A	G	GT:BD:BK:BI:BVT:BLT:QQ	0|1:TP:gm:ti:SNP:het:100	0/1:TP:gm:ti:SNP:het:100	CommonFN			yes	no	CNR2 is annotated on GRCh37 to include a large region downstream that has an erroneous extra unplaced contig on chr1 only in GRCh37 (chr1_gl000191_random) that interferes with mapping to a 106 kb region that includes part of CNR2 as well as other genes PNRC2 and SRSF10 not included in our medical gene list													0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:TP:gm:ti:SNP:het:30	0/1:TP:gm:ti:SNP:het:30	0|1:TP:gm:ti:SNP:het:9.4	0/1:TP:gm:ti:SNP:het:9.4	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1:24275433	23948943
Common		GRCh37			1	chr1	24276212	23949722	890	FN	C	T	GT:BD:BK:BI:BVT:BLT:QQ	1|0:TP:gm:ti:SNP:het:33.0111	0/1:TP:gm:ti:SNP:het:33.0111	CommonFN			yes	no	CNR2 is annotated on GRCh37 to include a large region downstream that has an erroneous extra unplaced contig on chr1 only in GRCh37 (chr1_gl000191_random) that interferes with mapping to a 106 kb region that includes part of CNR2 as well as other genes PNRC2 and SRSF10 not included in our medical gene list													1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:ti:SNP:het:30	0/1:TP:gm:ti:SNP:het:30	1|0:TP:gm:ti:SNP:het:23	0/1:TP:gm:ti:SNP:het:23	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1:24276212	23949722
Common		GRCh37			1	chr1	24277102	23950612	971	FN	ACAAT	A	GT:BD:BK:BI:BVT:BLT:QQ	1|1:TP:gm:d1_5:INDEL:homalt:100	1/1:TP:gm:d1_5:INDEL:homalt:100	CommonFN			yes	no	CNR2 is annotated on GRCh37 to include a large region downstream that has an erroneous extra unplaced contig on chr1 only in GRCh37 (chr1_gl000191_random) that interferes with mapping to a 106 kb region that includes part of CNR2 as well as other genes PNRC2 and SRSF10 not included in our medical gene list													1|1:FN:.:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:d1_5:INDEL:homalt:30	1/1:TP:gm:d1_5:INDEL:homalt:30	1|1:TP:gm:d1_5:INDEL:homalt:25	1/1:TP:gm:d1_5:INDEL:homalt:25	1|1:FN:.:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1:24277102	23950612
Common		GRCh37			1	chr1	24278073	23951583	208	FN	C	T	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:lm:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	CNR2 is annotated on GRCh37 to include a large region downstream that has an erroneous extra unplaced contig on chr1 only in GRCh37 (chr1_gl000191_random) that interferes with mapping to a 106 kb region that includes part of CNR2 as well as other genes PNRC2 and SRSF10 not included in our medical gene list													1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:lm:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:ti:SNP:het:30	0/1:TP:gm:ti:SNP:het:30	1|0:TP:gm:ti:SNP:het:32.8	0/1:TP:gm:ti:SNP:het:32.8	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:lm:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1:24278073	23951583
PacBio_gatk4	gatk4hc_HG002_15kb_20kb_52X_SequelII.vcf.gz	GRCh37	small-variants	INDEL	1	chr1	24278281	23951791	0	FN	CAG	C	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	yes	no		yes	no	CNR2 is annotated on GRCh37 to include a large region downstream that has an erroneous extra unplaced contig on chr1 only in GRCh37 (chr1_gl000191_random) that interferes with mapping to a 106 kb region that includes part of CNR2 as well as other genes PNRC2 and SRSF10 not included in our medical gene list																											1:24278281	23951791
Common		GRCh37			1	chr1	24278281	23951791	137	FN	CAG	C	GT:BD:BK:BI:BVT:BLT:QQ	1|0:TP:gm:d1_5:INDEL:het:25.6872	0/1:TP:gm:d1_5:INDEL:het:25.6872	CommonFN			yes	no	CNR2 is annotated on GRCh37 to include a large region downstream that has an erroneous extra unplaced contig on chr1 only in GRCh37 (chr1_gl000191_random) that interferes with mapping to a 106 kb region that includes part of CNR2 as well as other genes PNRC2 and SRSF10 not included in our medical gene list													1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:d1_5:INDEL:het:30	0/1:TP:gm:d1_5:INDEL:het:30	1|0:TP:gm:d1_5:INDEL:het:20.3	0/1:TP:gm:d1_5:INDEL:het:20.3	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1:24278281	23951791
Common		GRCh37			1	chr1	24278418	23951928	209	FN	T	G	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	CNR2 is annotated on GRCh37 to include a large region downstream that has an erroneous extra unplaced contig on chr1 only in GRCh37 (chr1_gl000191_random) that interferes with mapping to a 106 kb region that includes part of CNR2 as well as other genes PNRC2 and SRSF10 not included in our medical gene list													1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:tv:SNP:het:30	0/1:TP:gm:tv:SNP:het:30	1|0:TP:gm:tv:SNP:het:20	0/1:TP:gm:tv:SNP:het:20	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1:24278418	23951928
Common		GRCh37			1	chr1	24278627	23952137	952	FN	G	A	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	CNR2 is annotated on GRCh37 to include a large region downstream that has an erroneous extra unplaced contig on chr1 only in GRCh37 (chr1_gl000191_random) that interferes with mapping to a 106 kb region that includes part of CNR2 as well as other genes PNRC2 and SRSF10 not included in our medical gene list													1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:ti:SNP:het:30	0/1:TP:gm:ti:SNP:het:30	1|0:TP:gm:ti:SNP:het:21.8	0/1:TP:gm:ti:SNP:het:21.8	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1:24278627	23952137
PacBio_gatk4	gatk4hc_HG002_15kb_20kb_52X_SequelII.vcf.gz	GRCh37	small-variants	SNP	1	chr1	24279579	23953089	239	FN	G	A	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	yes	no		yes	no	CNR2 is annotated on GRCh37 to include a large region downstream that has an erroneous extra unplaced contig on chr1 only in GRCh37 (chr1_gl000191_random) that interferes with mapping to a 106 kb region that includes part of CNR2 as well as other genes PNRC2 and SRSF10 not included in our medical gene list																											1:24279579	23953089
Common		GRCh37			1	chr1	24279818	23953328	631	FN	C	T	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	CNR2 is annotated on GRCh37 to include a large region downstream that has an erroneous extra unplaced contig on chr1 only in GRCh37 (chr1_gl000191_random) that interferes with mapping to a 106 kb region that includes part of CNR2 as well as other genes PNRC2 and SRSF10 not included in our medical gene list													1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:ti:SNP:het:30	0/1:TP:gm:ti:SNP:het:30	1|0:TP:gm:ti:SNP:het:31.3	0/1:TP:gm:ti:SNP:het:31.3	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1:24279818	23953328
Common		GRCh37			1	chr1	24280449	23953959	271	FN	A	T	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	CNR2 is annotated on GRCh37 to include a large region downstream that has an erroneous extra unplaced contig on chr1 only in GRCh37 (chr1_gl000191_random) that interferes with mapping to a 106 kb region that includes part of CNR2 as well as other genes PNRC2 and SRSF10 not included in our medical gene list													1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:tv:SNP:het:30	0/1:TP:gm:tv:SNP:het:30	1|0:TP:gm:tv:SNP:het:27.4	0/1:TP:gm:tv:SNP:het:27.4	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1:24280449	23953959
Common		GRCh37			1	chr1	24280720	23954230	301	FN	C	T	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	CNR2 is annotated on GRCh37 to include a large region downstream that has an erroneous extra unplaced contig on chr1 only in GRCh37 (chr1_gl000191_random) that interferes with mapping to a 106 kb region that includes part of CNR2 as well as other genes PNRC2 and SRSF10 not included in our medical gene list													1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:ti:SNP:het:30	0/1:TP:gm:ti:SNP:het:30	1|0:TP:gm:ti:SNP:het:31.8	0/1:TP:gm:ti:SNP:het:31.8	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1:24280720	23954230
Common		GRCh37			1	chr1	24281021	23954531	989	FN	G	A	GT:BD:BK:BI:BVT:BLT:QQ	1|0:TP:gm:ti:SNP:het:18.3721	0/1:TP:gm:ti:SNP:het:18.3721	CommonFN			yes	no	CNR2 is annotated on GRCh37 to include a large region downstream that has an erroneous extra unplaced contig on chr1 only in GRCh37 (chr1_gl000191_random) that interferes with mapping to a 106 kb region that includes part of CNR2 as well as other genes PNRC2 and SRSF10 not included in our medical gene list													1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:ti:SNP:het:30	0/1:TP:gm:ti:SNP:het:30	1|0:TP:gm:ti:SNP:het:22.8	0/1:TP:gm:ti:SNP:het:22.8	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1:24281021	23954531
Common		GRCh37			1	chr1	24282010	23955520	652	FN	CAA	C	GT:BD:BK:BI:BVT:BLT:QQ	1|1:TP:gm:d1_5:INDEL:homalt:100	1/1:TP:gm:d1_5:INDEL:homalt:100	CommonFN			yes	no	CNR2 is annotated on GRCh37 to include a large region downstream that has an erroneous extra unplaced contig on chr1 only in GRCh37 (chr1_gl000191_random) that interferes with mapping to a 106 kb region that includes part of CNR2 as well as other genes PNRC2 and SRSF10 not included in our medical gene list													1|1:FN:.:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:d1_5:INDEL:homalt:30	1/1:TP:gm:d1_5:INDEL:homalt:30	1|1:TP:gm:d1_5:INDEL:homalt:35.8	1/1:TP:gm:d1_5:INDEL:homalt:35.8	1|1:FN:.:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1:24282010	23955520
Common		GRCh37			1	chr1	24282662	23956172	37	FN	T	A	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:lm:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	CNR2 is annotated on GRCh37 to include a large region downstream that has an erroneous extra unplaced contig on chr1 only in GRCh37 (chr1_gl000191_random) that interferes with mapping to a 106 kb region that includes part of CNR2 as well as other genes PNRC2 and SRSF10 not included in our medical gene list													1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:lm:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:tv:SNP:het:30	0/1:TP:gm:tv:SNP:het:30	1|0:TP:gm:tv:SNP:het:35.8	0/1:TP:gm:tv:SNP:het:35.8	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:lm:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1:24282662	23956172
Common		GRCh37			1	chr1	24282699	23956209	20	FN	C	CT	GT:BD:BK:BI:BVT:BLT:QQ	1|1:TP:gm:i1_5:INDEL:homalt:100	1/1:TP:gm:i1_5:INDEL:homalt:100	CommonFN			yes	no	CNR2 is annotated on GRCh37 to include a large region downstream that has an erroneous extra unplaced contig on chr1 only in GRCh37 (chr1_gl000191_random) that interferes with mapping to a 106 kb region that includes part of CNR2 as well as other genes PNRC2 and SRSF10 not included in our medical gene list													1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:i1_5:INDEL:homalt:30	1/1:TP:gm:i1_5:INDEL:homalt:30	1|1:FN:lm:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1:24282699	23956209
Common		GRCh37			1	chr1	24282719	23956229	339	FN	A	G	GT:BD:BK:BI:BVT:BLT:QQ	1|1:TP:gm:ti:SNP:homalt:100	1/1:TP:gm:ti:SNP:homalt:100	CommonFN			yes	no	CNR2 is annotated on GRCh37 to include a large region downstream that has an erroneous extra unplaced contig on chr1 only in GRCh37 (chr1_gl000191_random) that interferes with mapping to a 106 kb region that includes part of CNR2 as well as other genes PNRC2 and SRSF10 not included in our medical gene list													1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:ti:SNP:homalt:30	1/1:TP:gm:ti:SNP:homalt:30	1|1:TP:gm:ti:SNP:homalt:31.6	1/1:TP:gm:ti:SNP:homalt:31.6	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1:24282719	23956229
Common		GRCh37			1	chr1	24283058	23956568	1113	FN	TG	T	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	CNR2 is annotated on GRCh37 to include a large region downstream that has an erroneous extra unplaced contig on chr1 only in GRCh37 (chr1_gl000191_random) that interferes with mapping to a 106 kb region that includes part of CNR2 as well as other genes PNRC2 and SRSF10 not included in our medical gene list													1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:d1_5:INDEL:het:30	0/1:TP:gm:d1_5:INDEL:het:30	1|0:TP:gm:d1_5:INDEL:het:18.8	0/1:TP:gm:d1_5:INDEL:het:18.8	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1:24283058	23956568
Common		GRCh37			1	chr1	24284171	23957681	535	FN	AT	A,ATTT	GT:BD:BK:BI:BVT:BLT:QQ	1|2:FN:am:d1_5,i1_5:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:6.1206	CommonFN			yes	no	CNR2 is annotated on GRCh37 to include a large region downstream that has an erroneous extra unplaced contig on chr1 only in GRCh37 (chr1_gl000191_random) that interferes with mapping to a 106 kb region that includes part of CNR2 as well as other genes PNRC2 and SRSF10 not included in our medical gene list													1|2:FN:.:d1_5,i1_5:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:0	1|2:FN:.:d1_5,i1_5:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:0	1|2:TP:gm:d1_5,i1_5:INDEL:hetalt:30	0/1:TP:gm:d1_5:INDEL:het:30	1|2:FN:.:d1_5,i1_5:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:0	1|2:FN:am:d1_5,i1_5:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:0	1|2:FN:.:d1_5,i1_5:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:0	1|2:FN:am:d1_5,i1_5:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:16	1:24284171	23957681
Common		GRCh37			1	chr1	24284706	23958216	611	FN	A	G	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	CNR2 is annotated on GRCh37 to include a large region downstream that has an erroneous extra unplaced contig on chr1 only in GRCh37 (chr1_gl000191_random) that interferes with mapping to a 106 kb region that includes part of CNR2 as well as other genes PNRC2 and SRSF10 not included in our medical gene list													1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:ti:SNP:het:30	0/1:TP:gm:ti:SNP:het:30	1|0:TP:gm:ti:SNP:het:19.7	0/1:TP:gm:ti:SNP:het:19.7	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1:24284706	23958216
NYGC	HG-002-2x250-b37.recalibrated.haplotypeCalls.vcf.gz	GRCh37	small-variants	INDEL	1	chr1	24285317	23958827	204	FP_FN	GAATT	G	GT:BD:BK:QQ:BI:BVT:BLT	0|1:FN:am:.:d1_5:INDEL:het	1/1:FP:am:35.71:d1_5:INDEL:homalt 	yes	yes		yes	no	CNR2 is annotated on GRCh37 to include a large region downstream that has an erroneous extra unplaced contig on chr1 only in GRCh37 (chr1_gl000191_random) that interferes with mapping to a 106 kb region that includes part of CNR2 as well as other genes PNRC2 and SRSF10 not included in our medical gene list																											1:24285317	23958827
Common		GRCh37			1	chr1	24285521	23959031	1405236	FN	T	G	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	CNR2 is annotated on GRCh37 to include a large region downstream that has an erroneous extra unplaced contig on chr1 only in GRCh37 (chr1_gl000191_random) that interferes with mapping to a 106 kb region that includes part of CNR2 as well as other genes PNRC2 and SRSF10 not included in our medical gene list													1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:tv:SNP:het:30	0/1:TP:gm:tv:SNP:het:30	1|0:TP:gm:tv:SNP:het:21.5	0/1:TP:gm:tv:SNP:het:21.5	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1:24285521	23959031
Common		GRCh37			1	chr1	25690758	25364267	0	FN	C	T	GT:BD:BK:BI:BVT:BLT:QQ	0|1:TP:gm:ti:SNP:het:100	0/1:TP:gm:ti:SNP:het:100	CommonFN			yes		FN in short reads in segdup													0|1:TP:gm:ti:SNP:het:954.77	0/1:TP:gm:ti:SNP:het:954.77	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:TP:gm:ti:SNP:het:479.76	0/1:TP:gm:ti:SNP:het:479.76	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1:25690758	25364267
Common		GRCh38			1	chr1	25690758	25364267	3043	FN	C	T	GT:BD:BK:QQ:BI:BVT:BLT	0|1:TP:gm:100:ti:SNP:het	0/1:TP:gm:100:ti:SNP:het	CommonFN			yes		FN in short reads in segdup													0|1:TP:gm:954.77:ti:SNP:het	0/1:TP:gm:954.77:ti:SNP:het	0|1:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:TP:gm:456.23:ti:SNP:het	0/1:TP:gm:456.23:ti:SNP:het	0|1:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall		25690758
CMH_DRAGEN_3.6.3	NA24385.hard-filtered.vcf.gz	GRCh38	small-variants	SNP	1	chr1	25693801	25367310	38723	FN	C	G	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	yes	no	Aligned with poor mapping quality at the edge of SINE							skip																								25693801
BCM-HGSC_xAtlas	HG002.GRCh38.60x.1_merged.vcf.gz	GRCh38	small-variants	SNP	1	chr1	25732524	25406033	23	FN	A	G	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0 	Yes	No		yes	no	Complex set of variants in RHCE, which cause a sequence similar to part of RHD, so that short reads incorrectly align to RHD. This is a 4.5kb event that looks like a gene conversion, though it its biological origin may be different				skip																								25732524
Common		GRCh38			1	chr1	25732547	25406056	1	FN	T	C	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:100:ti:SNP:homalt	1/1:TP:gm:100:ti:SNP:homalt	CommonFN			yes	no	Complex set of variants in RHCE, which cause a sequence similar to part of RHD, so that short reads incorrectly align to RHD. This is a 4.5kb event that looks like a gene conversion, though it its biological origin may be different													1|1:TP:gm:2491.77:ti:SNP:homalt	1/1:TP:gm:2491.77:ti:SNP:homalt	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:TP:gm:30:ti:SNP:homalt	1/1:TP:gm:30:ti:SNP:homalt	1|1:FN:lm:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall		25732547
CMH_DRAGEN_3.6.3	NA24385.hard-filtered.vcf.gz	GRCh38	small-variants	SNP	1	chr1	25732548	25406057	122	FN	G	A	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	yes	no	Barely covered by short reads	yes	no	Complex set of variants in RHCE, which cause a sequence similar to part of RHD, so that short reads incorrectly align to RHD. This is a 4.5kb event that looks like a gene conversion, though it its biological origin may be different				skip																								25732548
Common		GRCh37			1	chr1	25732670	25406179	0	FN	TC	T	GT:BD:BK:BI:BVT:BLT:QQ	1|1:TP:gm:d1_5:INDEL:homalt:100	1/1:TP:gm:d1_5:INDEL:homalt:100	CommonFN			yes	no	Complex set of variants in RHCE, which cause a sequence similar to part of RHD, so that short reads incorrectly align to RHD. This is a 4.5kb event that looks like a gene conversion, though it its biological origin may be different													1|1:TP:gm:d1_5:INDEL:homalt:2392.73	1/1:TP:gm:d1_5:INDEL:homalt:2392.73	1|1:FN:.:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:d1_5:INDEL:homalt:30	1/1:TP:gm:d1_5:INDEL:homalt:30	1|1:FN:lm:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1:25732670	25406179
Common		GRCh38			1	chr1	25732670	25406179	81	FN	TC	T	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:100:d1_5:INDEL:homalt	1/1:TP:gm:100:d1_5:INDEL:homalt	CommonFN			yes	no	Complex set of variants in RHCE, which cause a sequence similar to part of RHD, so that short reads incorrectly align to RHD. This is a 4.5kb event that looks like a gene conversion, though it its biological origin may be different													1|1:TP:gm:2392.73:d1_5:INDEL:homalt	1/1:TP:gm:2392.73:d1_5:INDEL:homalt	1|1:FN:.:.:d1_5:INDEL:homalt	.:.:.:0:.:NOCALL:nocall	1|1:TP:gm:30:d1_5:INDEL:homalt	1/1:TP:gm:30:d1_5:INDEL:homalt	1|1:FN:lm:.:d1_5:INDEL:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:d1_5:INDEL:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:d1_5:INDEL:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:d1_5:INDEL:homalt	.:.:.:0:.:NOCALL:nocall		25732670
Common		GRCh37			1	chr1	25732751	25406260	42	FN	T	C	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:lm:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	Complex set of variants in RHCE, which cause a sequence similar to part of RHD, so that short reads incorrectly align to RHD. This is a 4.5kb event that looks like a gene conversion, though it its biological origin may be different													1|1:TP:gm:ti:SNP:homalt:2347.73	.:.:.:.:NOCALL:nocall:2347.73	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:ti:SNP:homalt:30	1/1:TP:gm:ti:SNP:homalt:30	1|1:TP:gm:ti:SNP:homalt:18.7	1/1:TP:gm:ti:SNP:homalt:18.7	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1:25732751	25406260
Common		GRCh37			1	chr1	25732793	25406302	0	FN	T	A	GT:BD:BK:BI:BVT:BLT:QQ	1|1:TP:gm:tv:SNP:homalt:100	1/1:TP:gm:tv:SNP:homalt:100	CommonFN			yes	no	Complex set of variants in RHCE, which cause a sequence similar to part of RHD, so that short reads incorrectly align to RHD. This is a 4.5kb event that looks like a gene conversion, though it its biological origin may be different													1|1:TP:gm:tv:SNP:homalt:2356.77	1/1:TP:gm:tv:SNP:homalt:2356.77	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:tv:SNP:homalt:30	1/1:TP:gm:tv:SNP:homalt:30	1|1:FN:lm:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1:25732793	25406302
Common		GRCh38			1	chr1	25732793	25406302	1	FN	T	A	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:100:tv:SNP:homalt	1/1:TP:gm:100:tv:SNP:homalt	CommonFN			yes	no	Complex set of variants in RHCE, which cause a sequence similar to part of RHD, so that short reads incorrectly align to RHD. This is a 4.5kb event that looks like a gene conversion, though it its biological origin may be different													1|1:TP:gm:2356.77:tv:SNP:homalt	1/1:TP:gm:2356.77:tv:SNP:homalt	1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:TP:gm:30:tv:SNP:homalt	1/1:TP:gm:30:tv:SNP:homalt	1|1:FN:lm:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall		25732793
Common		GRCh37			1	chr1	25732794	25406303	0	FN	A	T	GT:BD:BK:BI:BVT:BLT:QQ	1|1:TP:gm:tv:SNP:homalt:100	1/1:TP:gm:tv:SNP:homalt:100	CommonFN			yes	no	Complex set of variants in RHCE, which cause a sequence similar to part of RHD, so that short reads incorrectly align to RHD. This is a 4.5kb event that looks like a gene conversion, though it its biological origin may be different													1|1:TP:gm:tv:SNP:homalt:2356.77	1/1:TP:gm:tv:SNP:homalt:2356.77	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:tv:SNP:homalt:30	1/1:TP:gm:tv:SNP:homalt:30	1|1:FN:lm:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1:25732794	25406303
Common		GRCh38			1	chr1	25732794	25406303	326	FN	A	T	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:100:tv:SNP:homalt	1/1:TP:gm:100:tv:SNP:homalt	CommonFN			yes	no	Complex set of variants in RHCE, which cause a sequence similar to part of RHD, so that short reads incorrectly align to RHD. This is a 4.5kb event that looks like a gene conversion, though it its biological origin may be different													1|1:TP:gm:2356.77:tv:SNP:homalt	1/1:TP:gm:2356.77:tv:SNP:homalt	1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:TP:gm:30:tv:SNP:homalt	1/1:TP:gm:30:tv:SNP:homalt	1|1:FN:lm:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall		25732794
Common		GRCh37			1	chr1	25733120	25406629	1160	FN	GGT	G	GT:BD:BK:BI:BVT:BLT:QQ	1|1:TP:gm:d1_5:INDEL:homalt:27.9599	1/1:TP:gm:d1_5:INDEL:homalt:27.9599	CommonFN			yes	no	Complex set of variants in RHCE, which cause a sequence similar to part of RHD, so that short reads incorrectly align to RHD. This is a 4.5kb event that looks like a gene conversion, though it its biological origin may be different													1|1:TP:gm:d1_5:INDEL:homalt:2233.73	1/1:TP:gm:d1_5:INDEL:homalt:2233.73	1|1:FN:.:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:d1_5:INDEL:homalt:30	1/1:TP:gm:d1_5:INDEL:homalt:30	1|1:FN:lm:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1:25733120	25406629
BCM-HGSC_xAtlas	HG002.GRCh38.60x.1_merged.vcf.gz	GRCh38	small-variants	SNP	1	chr1	25734280	25407789	169	FN	C	T	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0 	Yes	No		yes	no	Complex set of variants in RHCE, which cause a sequence similar to part of RHD, so that short reads incorrectly align to RHD. This is a 4.5kb event that looks like a gene conversion, though it its biological origin may be different				skip																								25734280
BCM-HGSC_xAtlas	HG002.hs37d5.60x.1_merged.vcf.gz	GRCh37	small-variants	SNP	1	chr1	25734449	25407958	105	FN	T	C	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0 	Yes	No		yes	no	Complex set of variants in RHCE, which cause a sequence similar to part of RHD, so that short reads incorrectly align to RHD. This is a 4.5kb event that looks like a gene conversion, though it its biological origin may be different																											1:25734449	25407958
BCM-HGSC_xAtlas	HG002.hs37d5.60x.1_merged.vcf.gz	GRCh37	small-variants	SNP	1	chr1	25734554	25408063	229	FN	C	G	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0 	Yes	No		yes	no	Complex set of variants in RHCE, which cause a sequence similar to part of RHD, so that short reads incorrectly align to RHD. This is a 4.5kb event that looks like a gene conversion, though it its biological origin may be different																											1:25734554	25408063
CMH_DRAGEN_3.6.3	NA24385.hard-filtered.vcf.gz	GRCh37	small-variants	INDEL	1	chr1	25734783	25408292	0	FN	AAG	A	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:.:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	yes	no		yes	no	Complex set of variants in RHCE, which cause a sequence similar to part of RHD, so that short reads incorrectly align to RHD. This is a 4.5kb event that looks like a gene conversion, though it its biological origin may be different																											1:25734783	25408292
Common		GRCh37			1	chr1	25734783	25408292	0	FN	AAG	A	GT:BD:BK:BI:BVT:BLT:QQ	1|1:TP:gm:d1_5:INDEL:homalt:100	1/1:TP:gm:d1_5:INDEL:homalt:100	CommonFN			yes	no	Complex set of variants in RHCE, which cause a sequence similar to part of RHD, so that short reads incorrectly align to RHD. This is a 4.5kb event that looks like a gene conversion, though it its biological origin may be different													1|1:TP:gm:d1_5:INDEL:homalt:545.73	1/1:TP:gm:d1_5:INDEL:homalt:545.73	1|1:FN:.:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:d1_5:INDEL:homalt:30	1/1:TP:gm:d1_5:INDEL:homalt:30	1|1:FN:lm:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1:25734783	25408292
Common		GRCh38			1	chr1	25734783	25408292	1190	FN	AAG	A	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:100:d1_5:INDEL:homalt	1/1:TP:gm:100:d1_5:INDEL:homalt	CommonFN			yes	no	Complex set of variants in RHCE, which cause a sequence similar to part of RHD, so that short reads incorrectly align to RHD. This is a 4.5kb event that looks like a gene conversion, though it its biological origin may be different													1|1:TP:gm:545.73:d1_5:INDEL:homalt	1/1:TP:gm:545.73:d1_5:INDEL:homalt	1|1:FN:.:.:d1_5:INDEL:homalt	.:.:.:0:.:NOCALL:nocall	1|1:TP:gm:30:d1_5:INDEL:homalt	1/1:TP:gm:30:d1_5:INDEL:homalt	1|1:FN:lm:.:d1_5:INDEL:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:d1_5:INDEL:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:d1_5:INDEL:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:d1_5:INDEL:homalt	.:.:.:0:.:NOCALL:nocall		25734783
CMH_DRAGEN_3.6.3	NA24385.hard-filtered.vcf.gz	GRCh37	small-variants	SNP	1	chr1	25735973	25409482	48	FN	A	G	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	yes	no		yes	no	Complex set of variants in RHCE, which cause a sequence similar to part of RHD, so that short reads incorrectly align to RHD. This is a 4.5kb event that looks like a gene conversion, though it its biological origin may be different																											1:25735973	25409482
DNAnexus	GRCh38_HG002_WGS_union.vcf.gz	GRCh38	small-variants	SNP	1	chr1	25736021	25409530	74445233	FN	T	C	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0 	yes	no	Illumina - indicates 1 A 10x - indicates A,T,G as Alt calls as well  	yes	no	Complex set of variants in RHCE, which cause a sequence similar to part of RHD, so that short reads incorrectly align to RHD. This is a 4.5kb event that looks like a gene conversion, though it its biological origin may be different				skip																								25736021
ITER	ITERteam_small-variation_GRCh38_ILMN-PB-ONT.vcf.gz	GRCh38	small-variants	INDEL	1	chr1	100320319	99854763	1020467	FP_FN	C	CAAAAAA,CAAAAAAAAA	GT:BD:BK:QQ:BI:BVT:BLT	2|0:FN:lm:.:i6_15:INDEL:het	0/1:FP:lm:5.9:i6_15:INDEL:het	Yes	No	Repetitive region of polyAs. No support for 6nt query insertion, all technologies support 9nt truth insertion.							skip																								100320319
BCM-HGSC_xAtlas	HG002.hs37d5.60x.1_merged.vcf.gz	GRCh37	small-variants	INDEL	1	chr1	101340786	100875230	12208769	FN	GAC	G,GACACAC	GT:BD:BK:BI:BVT:BLT:QQ	2|1:FN:am:d1_5,i1_5:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:11 	Yes	No																															1:101340786	100875230
PacBio_gatk4	gatk4hc_HG002_15kb_20kb_52X_SequelII.vcf.gz	GRCh37	small-variants	INDEL	1	chr1	113626621	113083999	15245	FN	T	TAATAA,*	GT:BD:BK:BI:BVT:BLT:QQ	1|2:FN:lm:i1_5:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:0	yes	no	gatk calls a deltion, but this is complex.  Misses the other haplotype.																														1:113626621	113083999
Common		GRCh37			1	chr1	113641866	113099244	0	FP_FN	C	CTTTTTTTTT,CTTTTTTTTTT	GT:BD:BK:QQ:BI:BVT:BLT	2|2:FN:am:.:i6_15:INDEL:homalt	2/1:FP:am:100:i6_15:INDEL:hetalt	CommonFP_FN			no	yes	benchmark error likely due to noise in HiFi in 10/9bp insertion in homopolymer that makes in >20bp													2|2:FN:.:.:i6_15:INDEL:homalt	.:.:.:0:.:NOCALL:nocall	2|2:FN:lm:.:i6_15:INDEL:homalt	1/1:FP:lm:832.73:i6_15:INDEL:homalt	2|2:TP:gm:30:i6_15:INDEL:homalt	2/2:TP:gm:30:i6_15:INDEL:homalt	2|2:FN:am:.:i6_15:INDEL:homalt	2/1:FP:am:607.1:i6_15:INDEL:hetalt	2|2:TP:gm:0:i6_15:INDEL:homalt	2/2:TP:gm:0:i6_15:INDEL:homalt	2|2:FN:am:.:i6_15:INDEL:homalt	2/1:FP:am:210.28:i6_15:INDEL:hetalt	2|2:FN:lm:.:i6_15:INDEL:homalt	1/1:FP:lm:15:i6_15:INDEL:homalt	1:113641866	113099244
Common		GRCh38			1	chr1	113641866	113099244	2581441	FP_FN	C	CTTTTTTTTT,CTTTTTTTTTT	GT:BD:BK:QQ:BI:BVT:BLT	2|2:FN:am:.:i6_15:INDEL:homalt	2/1:FP:am:100:i6_15:INDEL:hetalt	CommonFP_FN			no	yes	benchmark error likely due to noise in HiFi in 10/9bp insertion in homopolymer that makes in >20bp													2|2:FN:.:.:i6_15:INDEL:homalt	.:.:.:0:.:NOCALL:nocall	2|2:FN:lm:.:i6_15:INDEL:homalt	1/1:FP:lm:833.73:i6_15:INDEL:homalt	2|2:TP:gm:30:i6_15:INDEL:homalt	2/2:TP:gm:30:i6_15:INDEL:homalt	2|2:FN:am:.:i6_15:INDEL:homalt	2/1:FP:am:796.1:i6_15:INDEL:hetalt	2|2:TP:gm:0:i6_15:INDEL:homalt	2/2:TP:gm:0:i6_15:INDEL:homalt	2|2:FN:am:.:i6_15:INDEL:homalt	2/1:FP:am:209.18:i6_15:INDEL:hetalt	2|2:FN:lm:.:i6_15:INDEL:homalt	1/1:FP:lm:15:i6_15:INDEL:homalt		113641866
DNAnexus	GRCh38_HG002_WGS_union.vcf.gz	GRCh38	small-variants	SNP	1	chr1	116223306	115680685	39600774	FN	T	G	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0 	yes	no								skip																								116223306
PacBio_gatk4	gatk4hc_HG002_15kb_20kb_52X_SequelII.vcf.gz	GRCh37	small-variants	SNP	1	chr1	155251250	155281459	6277095	FP_FN	T	C	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:ti:SNP:homalt	0/1:FP:am:981.31:ti:SNP:het	yes	no	seems like a common theme here is AluSx elements and regions around them																														1:155251250	155281459
DNAnexus	hs37d5_HG002_WGS_union.vcf.gz	GRCh37	small-variants	SNP	1	chr1	161528344	161558554	6888	FP_FN	G	T	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:tv:SNP:homalt	0/1:FP:am:0:tv:SNP:het	yes	no	Both long-read technologies (PacBio and ONT) suggest this position as homalt T/T, while both short-read technologies (Illumina and 10x) suggest this as homref G/G. Because this is self-chain region, I will follow what long-read's solution is suggestion. 																														1:161528344	161558554
BCM-HGSC_xAtlas	HG002.hs37d5.60x.1_merged.vcf.gz	GRCh37	small-variants	SNP	1	chr1	161535232	161565442	7114	FP_FN	A	G	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:ti:SNP:homalt	0/1:FP:am:31:ti:SNP:het 	Yes	No																															1:161535232	161565442
Common		GRCh37			1	chr1	161542346	161572556	568	FP_FN	C	T	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:39.9993:ti:SNP:homalt	1/1:TP:gm:39.9993:ti:SNP:homalt	CommonFP_FN			yes		mapping error from short reads													1|1:TP:gm:1886.77:ti:SNP:homalt	1/1:TP:gm:1886.77:ti:SNP:homalt	1|1:FN:am:.:ti:SNP:homalt	0/1:FP:am:1033.77:ti:SNP:het	1|1:TP:gm:30:ti:SNP:homalt	1/1:TP:gm:30:ti:SNP:homalt	1|1:FN:am:.:ti:SNP:homalt	0/1:FP:am:1551.6:ti:SNP:het	1|1:FN:am:.:ti:SNP:homalt	0/1:FP:am:0:ti:SNP:het	1|1:FN:am:.:ti:SNP:homalt	0/1:FP:am:40.23:ti:SNP:het	1|1:FN:am:.:ti:SNP:homalt	0/1:FP:am:33:ti:SNP:het	1:161542346	161572556
NYGC	HG-002-2x250-b37.recalibrated.haplotypeCalls.vcf.gz	GRCh37	small-variants	SNP	1	chr1	161542914	161573124	5802	FP_FN	T	C	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:ti:SNP:homalt	0/1:FP:am:1331.77:ti:SNP:het 	no	yes	There is clear evidence for the reference allele in the high coverage Illumina data and some evidence for it in the Pacbio CCS and ONT data. There is a SNV few bps upstream from this variant which seems to be on the other haplotype and evidence for the variant can be seen on all the platforms but it is not see in the Pacbio Hifi assembly data.	yes	no	benchmark appears likely correct since ONT supports homvar (except noisy reads) and HiFi ref reads have low MQ, but also homozygous region																											1:161542914	161573124
Common		GRCh37			1	chr1	161548716	161578926	149	FP_FN	G	A	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:ti:SNP:homalt	0/1:FP:am:36.989:ti:SNP:het	CommonFP_FN			yes		benchmark appears likely correct since ONT supports homvar (except noisy reads) and HiFi ref reads have low MQ, but also homozygous region													1|1:TP:gm:872.77:ti:SNP:homalt	1/1:TP:gm:872.77:ti:SNP:homalt	1|1:FN:am:.:ti:SNP:homalt	0/1:FP:am:742.77:ti:SNP:het	1|1:TP:gm:30:ti:SNP:homalt	1/1:TP:gm:30:ti:SNP:homalt	1|1:TP:gm:376.29:ti:SNP:homalt	1/1:TP:gm:376.29:ti:SNP:homalt	1|1:FN:am:.:ti:SNP:homalt	0/1:FP:am:0:ti:SNP:het	1|1:FN:am:.:ti:SNP:homalt	0/1:FP:am:32.65:ti:SNP:het	1|1:FN:am:.:ti:SNP:homalt	0/1:FP:am:25:ti:SNP:het	1:161548716	161578926
ITER	ITERteam_small-variation_GRCh37_ILMN-PB-ONT.vcf.gz	GRCh37	small-variants	INDEL	1	chr1	161548865	161579075	170	FP_FN	AG	A	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:252.01:d1_5:INDEL:het	Unsure	Unsure	There are reads that support both SNP, a deletion of 1nt and a deletion of 4nt.	unsure	unsure	benchmark may miss one haplotype due to homozygous region, but the one haplotype has low hifi coverage with low MQ, and unclear support from ONT																											1:161548865	161579075
Common		GRCh37			1	chr1	161549035	161579245	2210	FN	GAAAGT	G	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:.:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	CommonFN			unsure	unsure	benchmark may miss one haplotype due to homozygous region, but the one haplotype has low hifi coverage with low MQ, and unclear support from ONT													1|1:TP:gm:d1_5:INDEL:homalt:997.73	1/1:TP:gm:d1_5:INDEL:homalt:997.73	1|1:FN:.:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:d1_5:INDEL:homalt:30	1/1:TP:gm:d1_5:INDEL:homalt:30	1|1:FN:.:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1:161549035	161579245
Roche	RN_HG002_Illumina_PacBio_Oxford_GRCh37.vcf.gz	GRCh37	small-variants	SNP	1	chr1	161551245	161581455	6314	FP_FN	C	T	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:ti:SNP:homalt	0/1:FP:am:100:ti:SNP:het 	yes	no																															1:161551245	161581455
Common		GRCh37			1	chr1	161557559	161587769	6	FN	C	CAAAATAAAATAAAATAAAATAAAAT	GT:BD:BK:BI:BVT:BLT:QQ	1|1:TP:gm:i16_plus:INDEL:homalt:100	1/1:TP:gm:i16_plus:INDEL:homalt:100	CommonFN			yes		benchmark appears correct since supported by long reads													1|1:TP:gm:i16_plus:INDEL:homalt:1177.73	1/1:TP:gm:i16_plus:INDEL:homalt:1177.73	1|1:FN:.:i16_plus:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:i16_plus:INDEL:homalt:30	1/1:TP:gm:i16_plus:INDEL:homalt:30	1|1:FN:lm:i16_plus:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:lm:i16_plus:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:i16_plus:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:i16_plus:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1:161557559	161587769
Common		GRCh37			1	chr1	161557565	161587775	6541	FN	G	A	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:lm:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes		benchmark appears correct since supported by long reads													1|1:TP:gm:ti:SNP:homalt:1186.77	1/1:TP:gm:ti:SNP:homalt:1186.77	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:ti:SNP:homalt:30	1/1:TP:gm:ti:SNP:homalt:30	1|1:TP:gm:ti:SNP:homalt:44.9	1/1:TP:gm:ti:SNP:homalt:44.9	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1:161557565	161587775
Common		GRCh37			1	chr1	161564106	161594316	20693	FP	G	A	GT:QQ:BD:BK:BI:BVT:BLT	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	CommonFP			yes		likely mapping error from short and linked reads in seg dup													./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:632.77:FP:lm:ti:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:647.6:FP:lm:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:lm:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:25.42:FP:lm:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:24:FP:lm:ti:SNP:het	1:161564106	161594316
CMH_DRAGEN_3.6.3	NA24385.hard-filtered.vcf.gz	GRCh37	small-variants	SNP	1	chr1	161584799	161615009	0	FP_FN	A	T	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:tv:SNP:homalt	0/1:FP:am:42.88:tv:SNP:het	yes	no	Benchmark is  well-supported by PacBio only and it doesn't have two haplotag groups. Moreever, 10X supports the query pretty well and alleles are consistent among haplotags. However, I feel benchmark is more likely due to uneven coverage of query-supporting datasets such as 10X in the 5-10k bp bin	yes	no	likely mapping error from short reads																											1:161584799	161615009
NYGC	HG-002-2x250-b37.recalibrated.haplotypeCalls.vcf.gz	GRCh37	small-variants	SNP	1	chr1	161584799	161615009	27060	FP_FN	A	T	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:tv:SNP:homalt	0/1:FP:am:2047.77:tv:SNP:het 	yes	yes		yes	no	likely mapping error from short reads																											1:161584799	161615009
BCM-HGSC_xAtlas	HG002.hs37d5.60x.1_merged.vcf.gz	GRCh37	small-variants	SNP	1	chr1	161611859	161642069	551	FP_FN	C	G	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:tv:SNP:homalt	0/1:FP:am:22:tv:SNP:het 	Yes	No																															1:161611859	161642069
Common		GRCh37			1	chr1	161612410	161642620	66	FP_FN	C	T	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:100:ti:SNP:homalt	1/1:TP:gm:100:ti:SNP:homalt	CommonFP_FN			yes	no	likely mapping error from short reads													1|1:TP:gm:2721.77:ti:SNP:homalt	1/1:TP:gm:2721.77:ti:SNP:homalt	1|1:FN:am:.:ti:SNP:homalt	0/1:FP:am:1854.77:ti:SNP:het	1|1:TP:gm:30:ti:SNP:homalt	1/1:TP:gm:30:ti:SNP:homalt	1|1:FN:am:.:ti:SNP:homalt	0/1:FP:am:1021.6:ti:SNP:het	1|1:FN:am:.:ti:SNP:homalt	0/1:FP:am:0:ti:SNP:het	1|1:FN:am:.:ti:SNP:homalt	0/1:FP:am:45.07:ti:SNP:het	1|1:FN:am:.:ti:SNP:homalt	0/1:FP:am:38:ti:SNP:het	1:161612410	161642620
Common		GRCh37			1	chr1	161612476	161642686	11677	FP_FN	G	A	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:100:ti:SNP:homalt	1/1:TP:gm:100:ti:SNP:homalt	CommonFP_FN			yes	no	likely mapping error from short reads													1|1:TP:gm:2745.77:ti:SNP:homalt	1/1:TP:gm:2745.77:ti:SNP:homalt	1|1:FN:am:.:ti:SNP:homalt	0/1:FP:am:2106.77:ti:SNP:het	1|1:TP:gm:30:ti:SNP:homalt	1/1:TP:gm:30:ti:SNP:homalt	1|1:FN:am:.:ti:SNP:homalt	0/1:FP:am:659.6:ti:SNP:het	1|1:FN:am:.:ti:SNP:homalt	0/1:FP:am:0:ti:SNP:het	1|1:FN:am:.:ti:SNP:homalt	0/1:FP:am:45.08:ti:SNP:het	1|1:FN:am:.:ti:SNP:homalt	0/1:FP:am:27:ti:SNP:het	1:161612476	161642686
NYGC	HG-002-2x250-b37.recalibrated.haplotypeCalls.vcf.gz	GRCh37	small-variants	INDEL	1	chr1	161624153	161654363	0	FN	TG	T	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:.:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0 	yes	no		yes	no	likely mapping error from short reads																											1:161624153	161654363
Common		GRCh37			1	chr1	161624153	161654363	1679	FN	TG	T	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:lm:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	likely mapping error from short reads													1|1:TP:gm:d1_5:INDEL:homalt:1547.73	1/1:TP:gm:d1_5:INDEL:homalt:1547.73	1|1:FN:.:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:d1_5:INDEL:homalt:30	1/1:TP:gm:d1_5:INDEL:homalt:30	1|1:TP:gm:d1_5:INDEL:homalt:5.9	1/1:TP:gm:d1_5:INDEL:homalt:5.9	1|1:FN:.:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1:161624153	161654363
PacBio_gatk4	gatk4hc_HG002_15kb_20kb_52X_SequelII.vcf.gz	GRCh37	small-variants	SNP	1	chr1	161625832	161656042	45	FP_FN	A	C	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:tv:SNP:homalt	0/1:FP:am:1101.53:tv:SNP:het	yes	no	this is a little hard to interpret.  Low frequency variants here in all long/linked pileups	yes	no	hom var supported except some low MQ HiFi reads and noisy or short ONT reads																											1:161625832	161656042
PacBio_gatk4	gatk4hc_HG002_15kb_20kb_52X_SequelII.vcf.gz	GRCh37	small-variants	SNP	1	chr1	161625877	161656087	545	FP_FN	G	C	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:tv:SNP:homalt	0/1:FP:am:1094.53:tv:SNP:het	yes	no	seems like a common theme here is AluSx elements and regions around them	yes	no	hom var supported except some low MQ HiFi reads and noisy or short ONT reads																											1:161625877	161656087
DNAnexus	hs37d5_HG002_WGS_union.vcf.gz	GRCh37	small-variants	SNP	1	chr1	161626422	161656632	59	FP_FN	C	T	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:ti:SNP:homalt	0/1:FP:am:0:ti:SNP:het	unsure	yes	Both the benchmark and the query callset called this heterozygous INDEL. This should not be a FP. Instead, this is just a difference in how to genotype format is presented in the benchmark set and the query callset.	yes	no	hom var supported except some low MQ HiFi reads and noisy or short ONT reads																											1:161626422	161656632
PacBio_gatk4	gatk4hc_HG002_15kb_20kb_52X_SequelII.vcf.gz	GRCh37	small-variants	SNP	1	chr1	161626481	161656691	513	FP_FN	C	T	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:ti:SNP:homalt	0/1:FP:am:970.77:ti:SNP:het	yes	no	seems like a common theme here is AluSx elements and regions around them	yes	no	hom var supported except some low MQ HiFi reads and noisy or short ONT reads																											1:161626481	161656691
Roche	RN_HG002_Illumina_PacBio_Oxford_GRCh37.vcf.gz	GRCh37	small-variants	SNP	1	chr1	161626994	161657204	3762	FP_FN	C	T	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:ti:SNP:homalt	0/1:FP:am:100:ti:SNP:het 	yes	no		yes	no	hom var supported except some low MQ HiFi reads and noisy or short ONT reads																											1:161626994	161657204
Common		GRCh37			1	chr1	161630756	161660966	408	FP	T	G	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:.:tv:SNP:het	CommonFP			yes	no	hom ref supported except some low MQ HiFi reads and noisy or short ONT reads													.:.:.:.:.:NOCALL:nocall	0/1:169.77:FP:.:tv:SNP:het	.:.:.:.:.:NOCALL:nocall	1/1:504.77:FP:.:tv:SNP:homalt	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	1/1:0:FP:.:tv:SNP:homalt	.:.:.:.:.:NOCALL:nocall	1/1:49.04:FP:.:tv:SNP:homalt	.:.:.:.:.:NOCALL:nocall	0/1:34:FP:.:tv:SNP:het	1:161630756	161660966
BCM-HGSC_xAtlas	HG002.hs37d5.60x.1_merged.vcf.gz	GRCh37	small-variants	SNP	1	chr1	161631164	161661374	1748	FN	G	A	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:lm:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0 	Yes	No		yes	no	hom var supported except some low MQ HiFi reads and noisy or short ONT reads																											1:161631164	161661374
Common		GRCh37			1	chr1	161632912	161663122	137	FP_FN	T	A	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:tv:SNP:homalt	0/1:FP:am:35.2289:tv:SNP:het	CommonFP_FN			yes	no	hom var supported except some low MQ HiFi reads and noisy or short ONT reads													1|1:FN:am:.:tv:SNP:homalt	0/1:FP:am:949.77:tv:SNP:het	1|1:FN:am:.:tv:SNP:homalt	0/1:FP:am:97.77:tv:SNP:het	1|1:TP:gm:30:tv:SNP:homalt	1/1:TP:gm:30:tv:SNP:homalt	1|1:FN:am:.:tv:SNP:homalt	0/1:FP:am:203.72:tv:SNP:het	1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:am:.:tv:SNP:homalt	0/1:FP:am:13:tv:SNP:het	1:161632912	161663122
Roche	RN_HG002_Illumina_PacBio_Oxford_GRCh37.vcf.gz	GRCh37	small-variants	SNP	1	chr1	161633049	161663259	127	FP	C	T	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:13.5726:FP:.:ti:SNP:het 	yes	no		yes	no	hom ref supported except some low MQ HiFi reads and noisy or short ONT reads																											1:161633049	161663259
Roche	RN_HG002_Illumina_PacBio_Oxford_GRCh37.vcf.gz	GRCh37	small-variants	SNP	1	chr1	161633176	161663386	0	FP_FN	C	G	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:tv:SNP:homalt	0/1:FP:am:100:tv:SNP:het 	yes	no		yes	no	hom var supported except some low MQ HiFi reads and noisy or short ONT reads																											1:161633176	161663386
ITER	ITERteam_small-variation_GRCh37_ILMN-PB-ONT.vcf.gz	GRCh37	small-variants	SNP	1	chr1	161633176	161663386	0	FP_FN	C	G	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:tv:SNP:homalt	0/1:FP:am:272.7:tv:SNP:het	No	Yes	All technologies support het genotype. There are two more nearby variants in the same situation, truth called it as homalt and we called it as het.	yes	no	hom var supported except some low MQ HiFi reads and noisy or short ONT reads																											1:161633176	161663386
Common		GRCh37			1	chr1	161633176	161663386	0	FP_FN	C	G	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:tv:SNP:homalt	0/1:FP:am:100:tv:SNP:het	CommonFP_FN			yes	no	hom var supported except some low MQ HiFi reads and noisy or short ONT reads													1|1:FN:am:.:tv:SNP:homalt	0/1:FP:am:802.77:tv:SNP:het	1|1:FN:am:.:tv:SNP:homalt	0/1:FP:am:278.77:tv:SNP:het	1|1:TP:gm:30:tv:SNP:homalt	1/1:TP:gm:30:tv:SNP:homalt	1|1:FN:am:.:tv:SNP:homalt	0/1:FP:am:272.7:tv:SNP:het	1|1:FN:am:.:tv:SNP:homalt	0/1:FP:am:0:tv:SNP:het	1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:am:.:tv:SNP:homalt	0/1:FP:am:9:tv:SNP:het	1:161633176	161663386
Common		GRCh38			1	chr1	161633176	161663386	1769	FP_FN	C	G	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:tv:SNP:homalt	0/1:FP:am:100:tv:SNP:het	CommonFP_FN			yes	no	hom var supported except some low MQ HiFi reads and noisy or short ONT reads													1|1:FN:am:.:tv:SNP:homalt	0/1:FP:am:802.77:tv:SNP:het	1|1:FN:am:.:tv:SNP:homalt	0/1:FP:am:278.77:tv:SNP:het	1|1:TP:gm:30:tv:SNP:homalt	1/1:TP:gm:30:tv:SNP:homalt	1|1:FN:am:.:tv:SNP:homalt	0/1:FP:am:258.61:tv:SNP:het	1|1:FN:am:.:tv:SNP:homalt	0/1:FP:am:0:tv:SNP:het	1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:am:.:tv:SNP:homalt	0/1:FP:am:9:tv:SNP:het		161633176
NYGC	HG-002-2x250-b37.recalibrated.haplotypeCalls.vcf.gz	GRCh37	small-variants	SNP	1	chr1	161634945	161665155	24644980	FN	T	C	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0 	yes	no		yes	no	hom var supported except some low MQ HiFi reads and noisy or short ONT reads																											1:161634945	161665155
Common		GRCh37			1	chr1	186279267	186310135	0	FP_FN	T	TG,TGGG,TGG,TTG	GT:BD:BK:BI:QQ:BVT:BLT	2|1:FN:am:i1_5:.:INDEL:hetalt	3/1:FP:am:i1_5:100:INDEL:hetalt	CommonFP_FN			unsure		All techs are noisy in G homopolymer													2|1:FN:.:i1_5:.:INDEL:hetalt	.:.:.:.:0:NOCALL:nocall	2|1:FN:am:i1_5:.:INDEL:hetalt	1/1:FP:am:i1_5:212.73:INDEL:homalt	2|1:FN:am:i1_5:.:INDEL:hetalt	3/1:FP:am:i1_5:30:INDEL:hetalt	2|1:FN:.:i1_5:.:INDEL:hetalt	.:.:.:.:0:NOCALL:nocall	2|1:FN:am:i1_5:.:INDEL:hetalt	0/1:FP:am:i1_5:0:INDEL:het	2|1:FN:lm:i1_5:.:INDEL:hetalt	4/3:FP:lm:i1_5:49.78:INDEL:hetalt	2|1:FN:am:i1_5:.:INDEL:hetalt	1/1:FP:am:i1_5:13:INDEL:homalt	1:186279267	186310135
Common		GRCh38			1	chr1	186279267	186310135	12339236	FP_FN	T	TG,TGG,TGGG,TTG	GT:BD:BK:BI:QQ:BVT:BLT	3|1:FN:am:i1_5:.:INDEL:hetalt	2/1:FP:am:i1_5:100:INDEL:hetalt	CommonFP_FN			unsure		All techs are noisy in G homopolymer													3|1:FN:.:i1_5:.:INDEL:hetalt	.:.:.:.:0:NOCALL:nocall	3|1:FN:am:i1_5:.:INDEL:hetalt	1/1:FP:am:i1_5:179.73:INDEL:homalt	3|1:FN:am:i1_5:.:INDEL:hetalt	2/1:FP:am:i1_5:30:INDEL:hetalt	3|1:FN:am:i1_5:.:INDEL:hetalt	2/1:FP:am:i1_5:110.1:INDEL:hetalt	3|1:FN:am:i1_5:.:INDEL:hetalt	0/1:FP:am:i1_5:0:INDEL:het	3|1:FN:lm:i1_5:.:INDEL:hetalt	4/2:FP:lm:i1_5:47.49:INDEL:hetalt	3|1:FN:am:i1_5:.:INDEL:hetalt	1/1:FP:am:i1_5:13:INDEL:homalt		186279267
ITER	ITERteam_small-variation_GRCh38_ILMN-PB-ONT.vcf.gz	GRCh38	small-variants	SNP	1	chr1	198618500	198649371	46796	FP_FN	A	G	GT:BD:BK:QQ:BI:BVT:BLT	1|0:FN:am:.:ti:SNP:het	1/1:FP:am:10.8:ti:SNP:homalt	Yes	No	Het genotype well supported by all technologies in truth. Query reads have low MQ and fewer reads in comparison to truth.							skip																								198618500
Common		GRCh37			1	chr1	198665296	198696167	0	FP_FN	A	AAT	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:100:i1_5:INDEL:het	CommonFP_FN			no	yes	benchmark error in TR likely due to homozygous region													1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:637.73:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:835.73:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:30:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:486.64:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:0:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:50:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:14:i1_5:INDEL:het	1:198665296	198696167
Common		GRCh38			1	chr1	198665296	198696167	26945	FP_FN	A	AAT	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:100:i1_5:INDEL:het	CommonFP_FN			no	yes	benchmark error in TR likely due to homozygous region													1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:637.73:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:832.73:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:30:i1_5:INDEL:het	1|1:FN:.:.:i1_5:INDEL:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:0:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:50:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:14:i1_5:INDEL:het		198665296
PacBio_gatk4	gatk4hc_HG002_15kb_20kb_52X_SequelII.vcf.gz	GRCh37	small-variants	INDEL	1	chr1	198692241	198723112	-197691584	FP_FN	C	CAT	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:1320.73:i1_5:INDEL:het	yes	no																															1:198692241	198723112
CMH_DRAGEN_3.6.3	NA24385.hard-filtered.vcf.gz	GRCh37	small-variants	INDEL	2	chr2	1027214	1031528	68126	FP_FN	A	ATATATATATATATATATATATTTTTTT,ATATATATATATATATATATATATTTTTTT	GT:BD:BK:QQ:BI:BVT:BLT	2|0:FN:lm:.:i16_plus:INDEL:het	0/1:FP:lm:30.68:i16_plus:INDEL:het	yes	no	In simple repeat. The benchmark and query differ by repeating two bases AT. Not 100% sure but benchmark looks better because conflicting evidents mostly differ by the length of trailing homopolymer (Ts)																														2:1027214	1031528
DNAnexus	hs37d5_HG002_WGS_union.vcf.gz	GRCh37	small-variants	SNP	2	chr2	1095340	1099654	24052	FP	A	C	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:.:tv:SNP:het	no	yes	ONT, 10x, and Illumina raw reads all suggest the the existence of this variant, while only assembly and PacBio data suggested the opposite. The prior three raw data suggested that it is less likely a mapping error. We think this may be due to a base calling error in PacBio data.	yes	no	benchmark correctly calls 40bp ins in TR, which causes mismapped short/linked reads																											2:1095340	1099654
BCM-HGSC_xAtlas	HG002.GRCh38.60x.1_merged.vcf.gz	GRCh38	small-variants	INDEL	2	chr2	1119392	1123706	590	FP_FN	T	C,A	GT:BD:BK:BI:QQ:BVT:BLT	2|1:FN:am:ti,tv:.:SNP:hetalt	1/1:FP:am:ti:27:SNP:homalt 	Yes	No								skip																								1119392
Roche	RN_HG002_Illumina_PacBio_Oxford_GRCh37.vcf.gz	GRCh37	small-variants	INDEL	2	chr2	1119982	1124296	27013	FN	C	CTT	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:lm:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0 	yes	no																															2:1119982	1124296
DNAnexus	hs37d5_HG002_WGS_union.vcf.gz	GRCh37	small-variants	SNP	2	chr2	1146995	1151309	1815	FP	C	T	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:.:ti:SNP:het	no	yes	ONT, 10x, and Illumina raw reads all suggest the the existence of this variant, while only assembly and PacBio data suggested the opposite. The prior three raw data suggested that it is less likely a mapping error. We think this may be due to a base calling error in PacBio data.																														2:1146995	1151309
Common		GRCh37			2	chr2	1148810	1153124	0	FN	C	CA	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no	yes	likely hifiasm error due to noisy homopolymer													1|0:TP:gm:i1_5:INDEL:het:117.73	0/1:TP:gm:i1_5:INDEL:het:117.73	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	2:1148810	1153124
Common		GRCh38			2	chr2	1148810	1153124	27293	FN	C	CA	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no	yes	likely hifiasm error due to noisy homopolymer													1|0:TP:gm:i1_5:INDEL:het:117.73	0/1:TP:gm:i1_5:INDEL:het:117.73	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0		1148810
NCBI	HG002_grch38_dipcall.vcf.gz	GRCh38	small-variants	SNP	2	chr2	1176103	1180417	46988	FP_FN	A	G	GT:BD:BK:QQ:BI:BVT:BLT	1|0:FN:am:.:ti:SNP:het	1/1:FP:am:30:ti:SNP:homalt	yes	no	het correct; repeat							skip																								1176103
ITER	ITERteam_small-variation_GRCh38_ILMN-PB-ONT.vcf.gz	GRCh38	small-variants	SNP	2	chr2	1231175	1227405	476	FP_FN	G	C	GT:BD:BK:QQ:BI:BVT:BLT	0|1:FN:am:.:tv:SNP:het	1/1:FP:am:415.11:tv:SNP:homalt	Yes	No	Het genotype well supported by all technologies in truth. Query reads have low MQ and fewer reads in comparison to truth.							skip																								1231175
ITER	ITERteam_small-variation_GRCh38_ILMN-PB-ONT.vcf.gz	GRCh38	small-variants	SNP	2	chr2	1231651	1227881	38870	FP_FN	A	T	GT:BD:BK:QQ:BI:BVT:BLT	0|1:FN:am:.:tv:SNP:het	1/1:FP:am:415.14:tv:SNP:homalt	Yes	No	Het genotype well supported by all technologies in truth. Query reads have low MQ and fewer reads in comparison to truth.							skip																								1231651
Common		GRCh37			2	chr2	1270523	1266751	0	FP_FN	C	CTTTTTTT,CTTTTTTTTT	GT:BD:BK:BI:QQ:BVT:BLT	2|1:TP:gm:i6_15:100:INDEL:hetalt	2/1:TP:gm:i6_15:100:INDEL:hetalt	CommonFP_FN			unsure	no	Noisy insertions in long homopolymer that make it longer than 20 A's.  the average length on each haplotype is different, and illumina seems to support different lengths, so I think it's unlikely to be homvar like GATK calls													2|1:FN:am:i6_15:.:INDEL:hetalt	2/2:FP:am:i6_15:1855.73:INDEL:homalt	2|1:FN:am:i6_15:.:INDEL:hetalt	1/1:FP:am:i6_15:442.73:INDEL:homalt	2|1:FN:am:i6_15:.:INDEL:hetalt	2/2:FP:am:i6_15:30:INDEL:homalt	2|1:TP:gm:i6_15:545.1:INDEL:hetalt	2/1:TP:gm:i6_15:545.1:INDEL:hetalt	2|1:FN:am:i6_15:.:INDEL:hetalt	1/1:FP:am:i6_15:0:INDEL:homalt	2|1:TP:gm:i6_15:90.67:INDEL:hetalt	2/1:TP:gm:i6_15:90.67:INDEL:hetalt	2|1:FN:am:i6_15:.:INDEL:hetalt	1/1:FP:am:i6_15:11:INDEL:homalt	2:1270523	1266751
PacBio_gatk4	gatk4hc_HG002_15kb_20kb_53X_SequelII.vcf.gz	GRCh38	small-variants	INDEL	2	chr2	1270523	1266751	0	FP_FN	C	CTTTTTTTTT,CTTTTTTT	GT:BD:BK:BI:QQ:BVT:BLT	1|2:FN:am:i6_15:.:INDEL:hetalt	1/1:FP:am:i6_15:1855.73:INDEL:homalt	unsure	unsure	1bp differences in hompolymer expansion is impossible to judge from pileups	unsure	no	Noisy insertions in long homopolymer that make it longer than 20 A's.  the average length on each haplotype is different, and illumina seems to support different lengths, so I think it's unlikely to be homvar like GATK calls																												1270523
Common		GRCh38			2	chr2	1270523	1266751	19036	FP_FN	C	CTTTTTTT,CTTTTTTTTT,CTTTTT	GT:BD:BK:QQ:BI:BVT:BLT	2|1:TP:gm:100:i6_15:INDEL:hetalt	2/1:TP:gm:100:i6_15:INDEL:hetalt	CommonFP_FN			unsure	no	Noisy insertions in long homopolymer that make it longer than 20 A's.  the average length on each haplotype is different, and illumina seems to support different lengths, so I think it's unlikely to be homvar like GATK calls													2|1:FN:am:.:i6_15:INDEL:hetalt	2/2:FP:am:1855.73:i6_15:INDEL:homalt	2|1:TP:gm:526.73:i6_15:INDEL:hetalt	2/1:TP:gm:526.73:i6_15:INDEL:hetalt	2|1:FN:am:.:i6_15:INDEL:hetalt	2/2:FP:am:30:i6_15:INDEL:homalt	2|1:FN:am:.:i6_15:INDEL:hetalt	2/3:FP:am:12.6:i1_5,i6_15:INDEL:hetalt	2|1:FN:am:.:i6_15:INDEL:hetalt	1/1:FP:am:0:i6_15:INDEL:homalt	2|1:TP:gm:90.5:i6_15:INDEL:hetalt	2/1:TP:gm:90.5:i6_15:INDEL:hetalt	2|1:FN:am:.:i6_15:INDEL:hetalt	1/1:FP:am:11:i6_15:INDEL:homalt		1270523
PacBio_gatk4	gatk4hc_HG002_15kb_20kb_52X_SequelII.vcf.gz	GRCh37	small-variants	INDEL	2	chr2	1289559	1285787	4199	FP_FN	GT	G	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:1295.25:d1_5:INDEL:het	yes	no																															2:1289559	1285787
Common		GRCh37			2	chr2	1293758	1289986	0	FN	TA	T	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no	yes	likely consensus error in hifiasm since no support across techs													1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	2:1293758	1289986
Roche	RN_HG002_Illumina_PacBio_Oxford.vcf.gz	GRCh38	small-variants	INDEL	2	chr2	1293758	1289986	0	FN	TA	T	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0 	unsure	unsure	not visible from IGV pileups (only in the assembly)	no	yes	likely consensus error in hifiasm since no support across techs																												1293758
Common		GRCh38			2	chr2	1293758	1289986	8852	FN	TA	T	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no	yes	likely consensus error in hifiasm since no support across techs													1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0		1293758
Common		GRCh37			2	chr2	1302610	1298838	0	FP	AGCT	A	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:.:d1_5:INDEL:het	CommonFP			no	yes	benchmark misses haplotype likely due to homozygous region													.:.:.:.:.:NOCALL:nocall	0/1:873.73:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:864.73:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:685.6:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:50:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:15:FP:.:d1_5:INDEL:het	2:1302610	1298838
Common		GRCh38			2	chr2	1302610	1298838	13990	FP	AGCT	A	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:.:d1_5:INDEL:het	CommonFP			no	yes	benchmark misses haplotype likely due to homozygous region													.:.:.:.:.:NOCALL:nocall	0/1:876.73:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:866.73:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:972.6:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:50:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:15:FP:.:d1_5:INDEL:het		1302610
Common		GRCh37			2	chr2	1316600	1312828	0	FN	GT	G	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no	yes	likely consensus error in hifiasm since no support across techs													0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	2:1316600	1312828
Common		GRCh38			2	chr2	1316600	1312828	5063	FN	GT	G	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no	yes	likely consensus error in hifiasm since no support across techs													0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0		1316600
PacBio_gatk4	gatk4hc_HG002_15kb_20kb_53X_SequelII.vcf.gz	GRCh38	small-variants	SNP	2	chr2	1321663	1317891	84396	FN	G	A	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	yes	no								skip																								1321663
ITER	ITERteam_small-variation_GRCh38_ILMN-PB-ONT.vcf.gz	GRCh38	small-variants	SNP	2	chr2	1406059	1402287	15170	FN	A	G	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	Yes	No	All technologies in truth called this variant. Low MQ in query.							skip																								1406059
Common		GRCh37			2	chr2	1421229	1417457	0	FN	G	A	GT:BD:BK:BI:BVT:BLT:QQ	1|1:TP:gm:ti:SNP:homalt:100	1/1:TP:gm:ti:SNP:homalt:100	CommonFN			yes	no	missed in short reads due to long TR													1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:ti:SNP:homalt:30	1/1:TP:gm:ti:SNP:homalt:30	1|1:TP:gm:ti:SNP:homalt:500	1/1:TP:gm:ti:SNP:homalt:500	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	2:1421229	1417457
Common		GRCh38			2	chr2	1421229	1417457	41648	FN	G	A	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:39.9993:ti:SNP:homalt	1/1:TP:gm:39.9993:ti:SNP:homalt	CommonFN			yes	no	missed in short reads due to long TR													1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:TP:gm:30:ti:SNP:homalt	1/1:TP:gm:30:ti:SNP:homalt	1|1:TP:gm:500:ti:SNP:homalt	1/1:TP:gm:500:ti:SNP:homalt	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall		1421229
ITER	ITERteam_small-variation_GRCh38_ILMN-PB-ONT.vcf.gz	GRCh38	small-variants	SNP	2	chr2	1462877	1459105	718	FP	T	A	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:8.9:FP:lm:tv:SNP:het	Yes	No	No support in all technologies (Only detected by ONT reads, but with low depth and MQ). There is another homalt variant 8 positions ahead detected by both truth and query.							skip																								1462877
ITER	ITERteam_small-variation_GRCh38_ILMN-PB-ONT.vcf.gz	GRCh38	small-variants	SNP	2	chr2	1463595	1459823	198244	FN	C	T	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:lm:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	Yes	No	All technologies in truth called this variant. Low MQ in query.							skip																								1463595
ITER	ITERteam_small-variation_GRCh37_ILMN-PB-ONT.vcf.gz	GRCh37	small-variants	SNP	2	chr2	1661839	1658067	37375	FP_FN	T	C	GT:BD:BK:QQ:BI:BVT:BLT	0|1:FN:am:.:ti:SNP:het	1/1:FP:am:436.02:ti:SNP:homalt	Yes	No																															2:1661839	1658067
CMH_DRAGEN_3.6.3	NA24385.hard-filtered.vcf.gz	GRCh38	small-variants	SNP	2	chr2	1699214	1695442	26372	FP_FN	G	C	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:tv:SNP:homalt	0/1:FP:am:43.44:tv:SNP:het	yes	no								skip																								1699214
Common		GRCh37			2	chr2	1725586	1721814	0	FP	A	AAAAT	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:.:i1_5:INDEL:het	CommonFP			no	yes	benchmark misses haplotype likely due to homozygous region													.:.:.:.:.:NOCALL:nocall	0/1:424.73:FP:.:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:1035.73:FP:.:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:.:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:516.64:FP:.:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:.:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:50:FP:.:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:10:FP:.:i1_5:INDEL:het	2:1725586	1721814
Common		GRCh38			2	chr2	1725586	1721814	11934	FP	A	AAAAT	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:.:i1_5:INDEL:het	CommonFP			no	yes	benchmark misses haplotype likely due to homozygous region													.:.:.:.:.:NOCALL:nocall	0/1:424.73:FP:.:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:1035.73:FP:.:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:.:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:487.64:FP:.:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:.:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:50:FP:.:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:10:FP:.:i1_5:INDEL:het		1725586
NYGC	HG-002-2x250-b38.recalibrated.haplotypeCalls.vcf.gz	GRCh38	small-variants	INDEL	2	chr2	1737520	1733748	0	FP_FN	C	CAA,CAAA	GT:BD:BK:QQ:BI:BVT:BLT	2|2:FN:lm:.:i1_5:INDEL:homalt	1/1:FP:lm:350.77:i1_5:INDEL:homalt 	yes	yes		no	yes	benchmark misses one haplotype in homopolymer likely due to highly homozygous region																												1737520
Common		GRCh38			2	chr2	1737520	1733748	42140762	FP_FN	C	CAA,CAAA	GT:BD:BK:QQ:BI:BVT:BLT	2|2:FN:am:.:i1_5:INDEL:homalt	2/1:FP:am:100:i1_5:INDEL:hetalt	CommonFP_FN			no	yes	benchmark misses one haplotype in homopolymer likely due to highly homozygous region													2|2:FN:.:.:i1_5:INDEL:homalt	.:.:.:0:.:NOCALL:nocall	2|2:FN:lm:.:i1_5:INDEL:homalt	1/1:FP:lm:350.77:i1_5:INDEL:homalt	2|2:FN:am:.:i1_5:INDEL:homalt	2/1:FP:am:30:i1_5:INDEL:hetalt	2|2:FN:am:.:i1_5:INDEL:homalt	2/1:FP:am:205.1:i1_5:INDEL:hetalt	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	2|2:FN:am:.:i1_5:INDEL:homalt	2/1:FP:am:136.75:i1_5:INDEL:hetalt	2|2:TP:gm:5:i1_5:INDEL:homalt	2/2:TP:gm:5:i1_5:INDEL:homalt		1737520
DNAnexus	GRCh38_HG002_WGS_union.vcf.gz	GRCh38	small-variants	INDEL	2	chr2	44101649	43874510	44838610	FP	G	GC	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:lm:i1_5:INDEL:het 	yes	yes	The variants is called in the query callset, and presented as 1/2.	yes	no	benchmark clearly supported across techs, and query misses 2bp ins																												44101649
Common		GRCh37			2	chr2	89012638	88713120	0	FN	AT	A,ATTTTTT	GT:BD:BK:BI:BVT:BLT:QQ	2|1:FN:am:d1_5,i1_5:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:100	CommonFN			no	yes	benchmark likely has extra 1bp del in homopolymer adjacent to diTR due to noisy hifi reads													2|1:FN:am:d1_5,i1_5:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:484.73	2|1:FN:.:d1_5,i1_5:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:0	2|1:FN:.:d1_5,i1_5:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:0	2|1:FN:lm:d1_5,i1_5:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:5.9	2|1:FN:lm:d1_5,i1_5:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:0	2|1:FN:.:d1_5,i1_5:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:0	2|1:FN:am:d1_5,i1_5:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:6	2:89012638	88713120
PacBio_gatk4	gatk4hc_HG002_15kb_20kb_53X_SequelII.vcf.gz	GRCh38	small-variants	INDEL	2	chr2	89012638	88713120	0	FP	A	ATTTTT	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:484.73:FP:am:i1_5:INDEL:het	yes	no	Technically, both have the same call for this variant, but use a different reference (A->ATTTTT vs AT->ATTTTTT).  The GATK callset misses the delT at this position on the other allele, but for this record, the variants are equivalent.	no	yes	benchmark likely has extra 1bp del in homopolymer adjacent to diTR due to noisy hifi reads				skip																								89012638
Common		GRCh38			2	chr2	89012638	88713120	0	FN	AT	A,ATTTTTT	GT:BD:BK:BI:BVT:BLT:QQ	2|1:FN:am:d1_5,i1_5:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:100	CommonFN			no	yes	benchmark likely has extra 1bp del in homopolymer adjacent to diTR due to noisy hifi reads													2|1:FN:am:d1_5,i1_5:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:484.73	2|1:FN:am:d1_5,i1_5:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:93.25	2|1:FN:.:d1_5,i1_5:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:0	2|1:FN:am:d1_5,i1_5:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:25.64	2|1:FN:lm:d1_5,i1_5:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:0	2|1:FN:.:d1_5,i1_5:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:0	2|1:FN:am:d1_5,i1_5:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:6		89012638
Common		GRCh38			2	chr2	89012638	88713120	17687447	FP	A	ATTTTT	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:am:i1_5:INDEL:het	CommonFP			no	yes	benchmark likely has extra 1bp del in homopolymer adjacent to diTR due to noisy hifi reads													.:.:.:.:.:NOCALL:nocall	0/1:484.73:FP:am:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	1/1:93.25:FP:am:i1_5:INDEL:homalt	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:25.64:FP:am:i1_5:INDEL:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:6:FP:am:i1_5:INDEL:het		89012638
DNAnexus	GRCh38_HG002_WGS_union.vcf.gz	GRCh38	small-variants	SNP	2	chr2	107017023	106400567	16070	FN	G	A	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0 	yes	no								skip																								107017023
Common		GRCh37			2	chr2	107033093	106416637	0	FN	AT	A	GT:BD:BK:BI:BVT:BLT:QQ	1|0:TP:gm:d1_5:INDEL:het:100	0/1:TP:gm:d1_5:INDEL:het:100	CommonFN			yes	no	missed by some short reads due to segdup													1|0:TP:gm:d1_5:INDEL:het:918.73	0/1:TP:gm:d1_5:INDEL:het:918.73	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:d1_5:INDEL:het:30	0/1:TP:gm:d1_5:INDEL:het:30	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	2:107033093	106416637
NYGC	HG-002-2x250-b38.recalibrated.haplotypeCalls.vcf.gz	GRCh38	small-variants	INDEL	2	chr2	107033093	106416637	0	FN	AT	A	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0 	yes	no		yes	no	missed by some short reads due to segdup				skip																								107033093
Common		GRCh38			2	chr2	107033093	106416637	5316	FN	AT	A	GT:BD:BK:QQ:BI:BVT:BLT	1|0:TP:gm:100:d1_5:INDEL:het	0/1:TP:gm:100:d1_5:INDEL:het	CommonFN			yes	no	missed by some short reads due to segdup													1|0:TP:gm:918.73:d1_5:INDEL:het	0/1:TP:gm:918.73:d1_5:INDEL:het	1|0:FN:.:.:d1_5:INDEL:het	.:.:.:0:.:NOCALL:nocall	1|0:TP:gm:30:d1_5:INDEL:het	0/1:TP:gm:30:d1_5:INDEL:het	1|0:FN:.:.:d1_5:INDEL:het	.:.:.:0:.:NOCALL:nocall	1|0:FN:.:.:d1_5:INDEL:het	.:.:.:0:.:NOCALL:nocall	1|0:FN:.:.:d1_5:INDEL:het	.:.:.:0:.:NOCALL:nocall	1|0:FN:.:.:d1_5:INDEL:het	.:.:.:0:.:NOCALL:nocall		107033093
NCBI	HG002_grch37_dipcall.vcf.gz	GRCh37	small-variants	SNP	2	chr2	107038409	106421953	16373	FP	G	A	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	1/1:30:FP:.:ti:SNP:homalt	yes	no	segdup region																														2:107038409	106421953
Roche	RN_HG002_Illumina_PacBio_Oxford_GRCh37.vcf.gz	GRCh37	small-variants	INDEL	2	chr2	107054782	106438326	1107	FN	TA	T	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:.:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0 	yes	no																															2:107054782	106438326
Common		GRCh37			2	chr2	107055889	106439433	0	FP_FN	T	C	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:ti:SNP:homalt	0/1:FP:am:16.8001:ti:SNP:het	CommonFP_FN			no	yes	unsure why hifiasm misses haplotype													1|1:FN:am:.:ti:SNP:homalt	0/1:FP:am:725.77:ti:SNP:het	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:am:.:ti:SNP:homalt	0/1:FP:am:30:ti:SNP:het	1|1:FN:am:.:ti:SNP:homalt	0/1:FP:am:378.91:ti:SNP:het	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:am:.:ti:SNP:homalt	0/1:FP:am:20:ti:SNP:het	2:107055889	106439433
Common		GRCh38			2	chr2	107055889	106439433	10869	FP_FN	T	C	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:ti:SNP:homalt	0/1:FP:am:33.9806:ti:SNP:het	CommonFP_FN			no	yes	unsure why hifiasm misses haplotype													1|1:FN:am:.:ti:SNP:homalt	0/1:FP:am:747.77:ti:SNP:het	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:am:.:ti:SNP:homalt	0/1:FP:am:30:ti:SNP:het	1|1:FN:am:.:ti:SNP:homalt	0/1:FP:am:380.3:ti:SNP:het	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:am:.:ti:SNP:homalt	0/1:FP:am:20:ti:SNP:het		107055889
NCBI	HG002_grch37_dipcall.vcf.gz	GRCh37	small-variants	SNP	2	chr2	107066758	106450302	3349	FP_FN	A	C	GT:BD:BK:QQ:BI:BVT:BLT	1|0:FN:am:.:tv:SNP:het	1/1:FP:am:30:tv:SNP:homalt	yes	no	evidence for HET; segdup; adjacent SNP here																														2:107066758	106450302
BCM-HGSC_xAtlas	HG002.hs37d5.60x.1_merged.vcf.gz	GRCh37	small-variants	SNP	2	chr2	107070107	106453651	1899	FN	C	G	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0 	Yes	No																															2:107070107	106453651
NCBI	HG002_grch38_dipcall.vcf.gz	GRCh38	small-variants	SNP	2	chr2	107072006	106455550	2920	FP_FN	G	A	GT:BD:BK:QQ:BI:BVT:BLT	1|0:FN:am:.:ti:SNP:het	1/1:FP:am:30:ti:SNP:homalt	yes	no	het correct; segdup							skip																								107072006
NCBI	HG002_grch38_dipcall.vcf.gz	GRCh38	small-variants	SNP	2	chr2	107074926	106458470	94740069	FP_FN	T	C	GT:BD:BK:QQ:BI:BVT:BLT	1|0:FN:am:.:ti:SNP:het	1/1:FP:am:30:ti:SNP:homalt	yes	no	het correct; segdup							skip																								107074926
Common		GRCh37			2	chr2	202063262	201198539	40560230	FN	C	CTT	GT:BD:BK:BI:BVT:BLT:QQ	1|0:TP:gm:i1_5:INDEL:het:100	0/1:TP:gm:i1_5:INDEL:het:100	CommonFN			yes	no	benchmark supported by PCR-free illumina and HiFi in long homopolymer													1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:i1_5:INDEL:het:82.73	0/1:TP:gm:i1_5:INDEL:het:82.73	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:i1_5:INDEL:het:49.91	0/1:TP:gm:i1_5:INDEL:het:49.91	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	2:202063262	201198539
Common		GRCh37			2	chr2	242698184	241758769	0	FP_FN	A	ATGTG,ATGTGTG	GT:BD:BK:QQ:BI:BVT:BLT	2|2:FN:am:.:i6_15:INDEL:homalt	2/1:FP:am:100:i1_5,i6_15:INDEL:hetalt	CommonFP_FN			no	yes	PCR-free illumina supports het 2bp/4bp ins in TR, and HiFi is noisy, so benchmark is likely wrong													2|2:TP:gm:746.73:i6_15:INDEL:homalt	2/2:TP:gm:746.73:i6_15:INDEL:homalt	2|2:FN:am:.:i6_15:INDEL:homalt	2/1:FP:am:968.73:i1_5,i6_15:INDEL:hetalt	2|2:FN:am:.:i6_15:INDEL:homalt	2/1:FP:am:30:i1_5,i6_15:INDEL:hetalt	2|2:FN:am:.:i6_15:INDEL:homalt	2/1:FP:am:569.1:i1_5,i6_15:INDEL:hetalt	2|2:FN:am:.:i6_15:INDEL:homalt	2/1:FP:am:0:i1_5,i6_15:INDEL:hetalt	2|2:FN:am:.:i6_15:INDEL:homalt	2/1:FP:am:162.75:i1_5,i6_15:INDEL:hetalt	2|2:FN:lm:.:i6_15:INDEL:homalt	0/1:FP:lm:7:i1_5:INDEL:het	2:242698184	241758769
CMH_DRAGEN_3.6.3	NA24385.hard-filtered.vcf.gz	GRCh38	small-variants	INDEL	2	chr2	242698184	241758769	0	FP_FN	A	ATGTG,ATGTGTG	GT:BD:BK:QQ:BI:BVT:BLT	2|2:FN:am:.:i6_15:INDEL:homalt	2/1:FP:am:164.58:i1_5,i6_15:INDEL:hetalt	unsure	unsure	Confliting evidences exist in most datasets. At the edge of a repeat.	no	yes	PCR-free illumina supports het 2bp/4bp ins in TR, and HiFi is noisy, so benchmark is likely wrong																												242698184
Common		GRCh38			2	chr2	242698184	241758769	-241553665	FP_FN	A	ATGTG,ATGTGTG	GT:BD:BK:QQ:BI:BVT:BLT	2|2:FN:am:.:i6_15:INDEL:homalt	2/1:FP:am:100:i1_5,i6_15:INDEL:hetalt	CommonFP_FN			no	yes	PCR-free illumina supports het 2bp/4bp ins in TR, and HiFi is noisy, so benchmark is likely wrong													2|2:TP:gm:746.73:i6_15:INDEL:homalt	2/2:TP:gm:746.73:i6_15:INDEL:homalt	2|2:FN:am:.:i6_15:INDEL:homalt	2/1:FP:am:912.73:i1_5,i6_15:INDEL:hetalt	2|2:FN:am:.:i6_15:INDEL:homalt	2/1:FP:am:30:i1_5,i6_15:INDEL:hetalt	2|2:FN:am:.:i6_15:INDEL:homalt	2/1:FP:am:673.1:i1_5,i6_15:INDEL:hetalt	2|2:FN:am:.:i6_15:INDEL:homalt	2/1:FP:am:0:i1_5,i6_15:INDEL:hetalt	2|2:FN:am:.:i6_15:INDEL:homalt	2/1:FP:am:164.58:i1_5,i6_15:INDEL:hetalt	2|2:FN:lm:.:i6_15:INDEL:homalt	0/1:FP:lm:7:i1_5:INDEL:het		242698184
DNAnexus	hs37d5_HG002_WGS_union.vcf.gz	GRCh37	small-variants	INDEL	3	chr3	246787	205104	9854	FP_FN	C	CTTTCT	GT:BD:BK:QQ:BI:BVT:BLT	0|1:FN:am:.:i1_5:INDEL:het	1/1:FP:am:0:i1_5:INDEL:homalt	yes	yes	Both are representing the same insertion variance. The difference is due to (1) the presentation format and (2) the query callset is a union set of 4 different callers, so we are seeing more variant presentations of the same variant.	yes	no	genotype in query column being compared is incorrect																											3:246787	205104
DNAnexus	hs37d5_HG002_WGS_union.vcf.gz	GRCh37	small-variants	INDEL	3	chr3	256641	214958	37403	FP	A	ACACA	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:lm:i1_5:INDEL:het	unsure	yes	Simple Repeat region	yes	no	benchmark correctly calls 4bp ins and 2bp del in diTR																											3:256641	214958
ITER	ITERteam_small-variation_GRCh37_ILMN-PB-ONT.vcf.gz	GRCh37	small-variants	INDEL	3	chr3	294044	252361	0	FN	GAT	G,GATATAT	GT:BD:BK:BI:BVT:BLT:QQ	1|2:FN:am:d1_5,i1_5:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:952.64	Yes	No		no	yes	benchmark incorrectly has 2bp del on one TR haplotype due to noise in HiFi reads																											3:294044	252361
Common		GRCh37			3	chr3	294044	252361	0	FP	G	GATAT	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:am:i1_5:INDEL:het	CommonFP			no	yes	benchmark incorrectly has 2bp del on one TR haplotype due to noise in HiFi reads													.:.:.:.:.:NOCALL:nocall	0/1:262.73:FP:am:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:238.73:FP:am:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:am:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:952.64:FP:am:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:am:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:43.97:FP:am:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:11:FP:am:i1_5:INDEL:het	3:294044	252361
Common		GRCh37			3	chr3	294044	252361	0	FN	GAT	G,GATATAT	GT:BD:BK:BI:BVT:BLT:QQ	1|2:FN:am:d1_5,i1_5:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:100	CommonFN			no	yes	benchmark incorrectly has 2bp del on one TR haplotype due to noise in HiFi reads													1|2:FN:am:d1_5,i1_5:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:262.73	1|2:FN:am:d1_5,i1_5:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:238.73	1|2:FN:am:d1_5,i1_5:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:30	1|2:FN:am:d1_5,i1_5:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:952.64	1|2:FN:am:d1_5,i1_5:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:0	1|2:FN:am:d1_5,i1_5:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:43.97	1|2:FN:am:d1_5,i1_5:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:11	3:294044	252361
Roche	RN_HG002_Illumina_PacBio_Oxford.vcf.gz	GRCh38	small-variants	INDEL	3	chr3	294044	252361	0	FP	G	GATAT	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:am:i1_5:INDEL:het 	yes	yes	It seems that the benchmark is correct, but what we miss is not the ins but the 2-base deletion	no	yes	benchmark incorrectly has 2bp del on one TR haplotype due to noise in HiFi reads																												294044
Common		GRCh38			3	chr3	294044	252361	0	FN	GAT	G,GATATAT	GT:BD:BK:BI:BVT:BLT:QQ	1|2:FN:am:d1_5,i1_5:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:100	CommonFN			no	yes	benchmark incorrectly has 2bp del on one TR haplotype due to noise in HiFi reads													1|2:FN:am:d1_5,i1_5:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:262.73	1|2:FN:am:d1_5,i1_5:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:107.73	1|2:FN:am:d1_5,i1_5:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:30	1|2:FN:am:d1_5,i1_5:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:55.64	1|2:FN:am:d1_5,i1_5:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:0	1|2:FN:am:d1_5,i1_5:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:43.97	1|2:FN:am:d1_5,i1_5:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:10		294044
Common		GRCh38			3	chr3	294044	252361	35982	FP	G	GATAT	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:am:i1_5:INDEL:het	CommonFP			no	yes	benchmark incorrectly has 2bp del on one TR haplotype due to noise in HiFi reads													.:.:.:.:.:NOCALL:nocall	0/1:262.73:FP:am:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:107.73:FP:am:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:am:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:55.64:FP:am:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:am:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:43.97:FP:am:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:10:FP:am:i1_5:INDEL:het		294044
NCBI	HG002_grch38_dipcall.vcf.gz	GRCh38	small-variants	INDEL	3	chr3	330026	288343	25986	FN	C	CAT	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:lm:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	yes	no	no segdup							skip																								330026
Common		GRCh37			3	chr3	356012	314329	0	FP_FN	G	GTATATATATA,GTA,GTATATATA	GT:BD:BK:QQ:BI:BVT:BLT	2|3:FN:am:.:i1_5,i6_15:INDEL:hetalt	1/2:FP:am:100:i1_5,i6_15:INDEL:hetalt	CommonFP_FN			no	yes	Likely error in ins length due to noisy HiFi reads in diTR													2|3:FN:am:.:i1_5,i6_15:INDEL:hetalt	0/2:FP:am:1022.73:i1_5:INDEL:het	2|3:FN:.:.:i1_5,i6_15:INDEL:hetalt	.:.:.:0:.:NOCALL:nocall	2|3:FN:am:.:i1_5,i6_15:INDEL:hetalt	1/2:FP:am:30:i1_5,i6_15:INDEL:hetalt	2|3:FN:am:.:i1_5,i6_15:INDEL:hetalt	1/2:FP:am:838.1:i1_5,i6_15:INDEL:hetalt	2|3:FN:am:.:i1_5,i6_15:INDEL:hetalt	1/2:FP:am:0:i1_5,i6_15:INDEL:hetalt	2|3:FN:.:.:i1_5,i6_15:INDEL:hetalt	.:.:.:0:.:NOCALL:nocall	2|3:FN:lm:.:i1_5,i6_15:INDEL:hetalt	0/1:FP:lm:11:i6_15:INDEL:het	3:356012	314329
CMH_DRAGEN_3.6.3	NA24385.hard-filtered.vcf.gz	GRCh38	small-variants	INDEL	3	chr3	356012	314329	0	FN	G	GTA,GTATATATA	GT:BD:BK:BI:BVT:BLT:QQ	1|2:FN:.:i1_5,i6_15:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:0	unsure	no	The alternative allele, GTATATATA, is not as well supported as GTATATATATA especially in ILMN datasets.	no	yes	Likely error in ins length due to noisy HiFi reads in diTR																												356012
Roche	RN_HG002_Illumina_PacBio_Oxford.vcf.gz	GRCh38	small-variants	INDEL	3	chr3	356012	314329	0	FP_FN	G	GTA,GTATATATATA,GTATATATA	GT:BD:BK:BI:QQ:BVT:BLT	1|3:FN:am:i1_5,i6_15:.:INDEL:hetalt	2/1:FP:am:i1_5,i6_15:100:INDEL:hetalt 	no	yes	to me (mostly from ILM reads that span the repeat region, the right prediction is G-> GTA,GTATATATATA)	no	yes	Likely error in ins length due to noisy HiFi reads in diTR																												356012
Common		GRCh38			3	chr3	356012	314329	16327130	FP_FN	G	GTA,GTATATATATA,GTATATATA	GT:BD:BK:BI:QQ:BVT:BLT	1|3:FN:am:i1_5,i6_15:.:INDEL:hetalt	2/1:FP:am:i1_5,i6_15:100:INDEL:hetalt	CommonFP_FN			no	yes	Likely error in ins length due to noisy HiFi reads in diTR													1|3:FN:am:i1_5,i6_15:.:INDEL:hetalt	0/1:FP:am:i1_5:1022.73:INDEL:het	1|3:FN:.:i1_5,i6_15:.:INDEL:hetalt	.:.:.:.:0:NOCALL:nocall	1|3:FN:am:i1_5,i6_15:.:INDEL:hetalt	2/1:FP:am:i1_5,i6_15:30:INDEL:hetalt	1|3:FN:am:i1_5,i6_15:.:INDEL:hetalt	2/1:FP:am:i1_5,i6_15:90.1:INDEL:hetalt	1|3:FN:am:i1_5,i6_15:.:INDEL:hetalt	2/1:FP:am:i1_5,i6_15:0:INDEL:hetalt	1|3:FN:.:i1_5,i6_15:.:INDEL:hetalt	.:.:.:.:0:NOCALL:nocall	1|3:FN:lm:i1_5,i6_15:.:INDEL:hetalt	0/2:FP:lm:i6_15:11:INDEL:het		356012
BCM-HGSC_xAtlas	HG002.GRCh38.60x.1_merged.vcf.gz	GRCh38	small-variants	INDEL	3	chr3	16682966	16641459	10	FP	CAGAGAGAG	C	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:9:FP:am:d6_15:INDEL:het 	Yes	No								skip																								16682966
BCM-HGSC_xAtlas	HG002.GRCh38.60x.1_merged.vcf.gz	GRCh38	small-variants	SNP	3	chr3	16682976	16641469	32752201	FP	G	C	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:22:FP:lm:tv:SNP:het 	Yes	No								skip																								16682976
CMH_DRAGEN_3.6.3	NA24385.hard-filtered.vcf.gz	GRCh37	small-variants	INDEL	3	chr3	49431103	49393670	7371	FN	CTCTCTCTGTG	C	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:lm:d6_15:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	yes	no	Pretty certain benchmark is correct based on PacBio and ILMN-novoalign, but query is very close and some conflicting evidences exist even in PacBio																														3:49431103	49393670
DNAnexus	hs37d5_HG002_WGS_union.vcf.gz	GRCh37	small-variants	INDEL	3	chr3	49438474	49401041	0	FP_FN	CAAAA	C,CAAAAAAAAAAAAAAAAAAA	GT:BD:BK:BI:QQ:BVT:BLT	2|1:FN:am:d1_5,i6_15:.:INDEL:hetalt	0/1:FP:am:d1_5:0:INDEL:het	unsure	no	This is right next to a homopolymer region (20 A's in the reference) The benchmark set (by PacBio) looks more correct than the query callset. However, ONT reads are suggesting mutlipe other complicated possibilities for this region. 	unsure	no	benchmark may be correct but very long insertion on one haplotype in long homopolymer makes data noisy																											3:49438474	49401041
Common		GRCh37			3	chr3	49438474	49401041	0	FP_FN	CAAAA	C,CAAAAAAAAAAAAAAAAAAA	GT:BD:BK:BI:QQ:BVT:BLT	2|1:FN:am:d1_5,i6_15:.:INDEL:hetalt	0/1:FP:am:d1_5:26.5781:INDEL:het	CommonFP_FN			unsure	no	benchmark may be correct but very long insertion on one haplotype in long homopolymer makes data noisy													2|1:FN:am:d1_5,i6_15:.:INDEL:hetalt	1/1:FP:am:d1_5:539.73:INDEL:homalt	2|1:TP:gm:d1_5,i6_15:533.73:INDEL:hetalt	0/1:TP:gm:d1_5:533.73:INDEL:het	2|1:FN:am:d1_5,i6_15:.:INDEL:hetalt	1/1:FP:am:d1_5:30:INDEL:homalt	2|1:FN:am:d1_5,i6_15:.:INDEL:hetalt	0/1:FP:am:d1_5:482.93:INDEL:het	2|1:FN:am:d1_5,i6_15:.:INDEL:hetalt	0/1:FP:am:d1_5:0:INDEL:het	2|1:FN:am:d1_5,i6_15:.:INDEL:hetalt	0/1:FP:am:d1_5:50:INDEL:het	2|1:FN:am:d1_5,i6_15:.:INDEL:hetalt	0/1:FP:am:d1_5:13:INDEL:het	3:49438474	49401041
Common		GRCh38			3	chr3	49438474	49401041	517	FP_FN	CAAAA	C,CAAAAAAAAAAAAAAAAAAA	GT:BD:BK:BI:QQ:BVT:BLT	2|1:FN:am:d1_5,i6_15:.:INDEL:hetalt	0/1:FP:am:d1_5:26.5781:INDEL:het	CommonFP_FN			unsure	no	benchmark may be correct but very long insertion on one haplotype in long homopolymer makes data noisy													2|1:FN:am:d1_5,i6_15:.:INDEL:hetalt	1/1:FP:am:d1_5:539.73:INDEL:homalt	2|1:FN:am:d1_5,i6_15:.:INDEL:hetalt	1/1:FP:am:d1_5:419.73:INDEL:homalt	2|1:FN:am:d1_5,i6_15:.:INDEL:hetalt	1/1:FP:am:d1_5:30:INDEL:homalt	2|1:FN:am:d1_5,i6_15:.:INDEL:hetalt	0/1:FP:am:d1_5:511.06:INDEL:het	2|1:FN:am:d1_5,i6_15:.:INDEL:hetalt	0/1:FP:am:d1_5:0:INDEL:het	2|1:FN:am:d1_5,i6_15:.:INDEL:hetalt	0/1:FP:am:d1_5:50:INDEL:het	2|1:FN:am:d1_5,i6_15:.:INDEL:hetalt	0/1:FP:am:d1_5:13:INDEL:het		49438474
Common		GRCh37			3	chr3	49438991	49401558	0	FP	CA	C	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:lm:d1_5:INDEL:het	CommonFP			no	yes	likely hifiasm error missing del on one haplotype due to noisy homopolymer													.:.:.:.:.:NOCALL:nocall	0/1:41.84:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:604.73:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:728.06:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:182.24:FP:lm:d1_5:INDEL:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	3:49438991	49401558
Common		GRCh38			3	chr3	49438991	49401558	79222484	FP	CA	C	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:lm:d1_5:INDEL:het	CommonFP			no	yes	likely hifiasm error missing del on one haplotype due to noisy homopolymer													.:.:.:.:.:NOCALL:nocall	0/1:41.84:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:606.73:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:348.06:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:182.4:FP:lm:d1_5:INDEL:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.		49438991
PacBio_gatk4	gatk4hc_HG002_15kb_20kb_53X_SequelII.vcf.gz	GRCh38	small-variants	INDEL	3	chr3	128342885	128624042	3728	FP	G	GC	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:437.73:FP:.:i1_5:INDEL:het	yes	no								skip																								128342885
ITER	ITERteam_small-variation_GRCh38_ILMN-PB-ONT.vcf.gz	GRCh38	small-variants	INDEL	3	chr3	128346613	128627770	159	FP_FN	C	CA,CAAA	GT:BD:BK:QQ:BI:BVT:BLT	0|2:FN:lm:.:i1_5:INDEL:het	0/1:FP:lm:4.7:i1_5:INDEL:het	Yes	No	Repetitive region of polyAs. 3nt insertion has better support than 1nt insertion.							skip																								128346613
DNAnexus	GRCh38_HG002_WGS_union.vcf.gz	GRCh38	small-variants	SNP	3	chr3	128346772	128627929	4797328	FP	C	G	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:.:tv:SNP:het 	yes	no	 ONT - 12% G calls Sequelll - 9% G calls  							skip																								128346772
Common		GRCh37			3	chr3	133144101	133425257	0	FN	TG	T	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:lm:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no	yes	look likely to be hifiasm consensus error since they all come from one HiFi read and aren't supported by illumina.													0|1:FN:lm:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	3:133144101	133425257
BCM-HGSC_xAtlas	HG002.GRCh38.60x.1_merged.vcf.gz	GRCh38	small-variants	INDEL	3	chr3	133144101	133425257	0	FN	TG	T	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:lm:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0 	No	Yes	Insufficient support for TG->T deletion in Illumina 60x, 10X phased or PacBio Sequel II alignments.	no	yes	look likely to be hifiasm consensus error since they all come from one HiFi read and aren't supported by illumina.																												133144101
Common		GRCh38			3	chr3	133144101	133425257	302	FN	TG	T	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:lm:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no	yes	look likely to be hifiasm consensus error since they all come from one HiFi read and aren't supported by illumina.													0|1:FN:lm:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0		133144101
Common		GRCh37			3	chr3	133144403	133425559	0	FN	CA	C	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:lm:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no	yes	look likely to be hifiasm consensus error since they all come from one HiFi read and aren't supported by illumina.													0|1:FN:lm:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	3:133144403	133425559
CMH_DRAGEN_3.6.3	NA24385.hard-filtered.vcf.gz	GRCh38	small-variants	INDEL	3	chr3	133144403	133425559	0	FN	CA	C	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:lm:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	unsure	unsure	In LTR. Not or very poorly supported in all datasets	no	yes	look likely to be hifiasm consensus error since they all come from one HiFi read and aren't supported by illumina.																												133144403
Common		GRCh38			3	chr3	133144403	133425559	21011	FN	CA	C	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:lm:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no	yes	look likely to be hifiasm consensus error since they all come from one HiFi read and aren't supported by illumina.													0|1:FN:lm:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0		133144403
NYGC	HG-002-2x250-b37.recalibrated.haplotypeCalls.vcf.gz	GRCh37	small-variants	INDEL	3	chr3	133165414	133446570	0	FN	TTATATATATATA	T	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:lm:d6_15:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0 	yes	no		no	yes	hifiasm incorrectly averages 8 and 16bp dels in TR																											3:133165414	133446570
Common		GRCh37			3	chr3	133165414	133446570	14	FN	TTATATATATATA	T	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:lm:d6_15:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no	yes	hifiasm incorrectly averages 8 and 16bp dels in TR													1|1:FN:lm:d6_15:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:lm:d6_15:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:lm:d6_15:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:lm:d6_15:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:lm:d6_15:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:lm:d6_15:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:lm:d6_15:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	3:133165414	133446570
Common		GRCh37			3	chr3	133165428	133446584	2816370	FN	A	T	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:lm:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no	yes	hifiasm incorrectly averages 8 and 16bp dels in TR													1|1:FN:lm:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:lm:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:lm:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:lm:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:lm:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:lm:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:lm:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	3:133165428	133446584
Common		GRCh37			3	chr3	135981796	136262954	0	FP	GT	G	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:.:d1_5:INDEL:het	CommonFP			no	yes	likely hifiasm error missing del on one haplotype due to noisy homopolymer													.:.:.:.:.:NOCALL:nocall	0/1:56.73:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:175.73:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:75.6:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	1/1:54.73:FP:.:d1_5:INDEL:homalt	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	3:135981796	136262954
Common		GRCh38			3	chr3	135981796	136262954	5142	FP	GT	G	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:.:d1_5:INDEL:het	CommonFP			no	yes	likely hifiasm error missing del on one haplotype due to noisy homopolymer													.:.:.:.:.:NOCALL:nocall	0/1:56.73:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:175.73:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:207.6:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	1/1:54.67:FP:.:d1_5:INDEL:homalt	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.		135981796
Common		GRCh37			3	chr3	135986938	136268096	2	FP	A	ATATG	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:lm:i1_5:INDEL:het	CommonFP			no	yes	in complex compound het in adjacent diTRs, benchmark has one 4bp ins as 2bp likely due to HiFi noise													.:.:.:.:.:NOCALL:nocall	0/1:607.73:FP:lm:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:471.73:FP:lm:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:lm:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:751.64:FP:lm:i1_5:INDEL:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:50:FP:lm:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:8:FP:lm:i1_5:INDEL:het	3:135986938	136268096
Common		GRCh37			3	chr3	135986940	136268098	22573	FN	A	ATG	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:lm:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no	yes	in complex compound het in adjacent diTRs, benchmark has one 4bp ins as 2bp likely due to HiFi noise													0|1:FN:lm:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	3:135986940	136268098
PacBio_gatk4	gatk4hc_HG002_15kb_20kb_52X_SequelII.vcf.gz	GRCh37	small-variants	INDEL	3	chr3	136009513	136290671	0	FN	G	GTTTTTTTTTT,GTTTTTTTTTTT	GT:BD:BK:BI:BVT:BLT:QQ	1|2:FN:.:i6_15:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:0	yes	no																															3:136009513	136290671
ITER	ITERteam_small-variation_GRCh37_ILMN-PB-ONT.vcf.gz	GRCh37	small-variants	INDEL	3	chr3	136009513	136290671	0	FP_FN	G	GTTTTTTTTTT,GTTTTTTTTTTT	GT:BD:BK:BI:QQ:BVT:BLT	1|2:FN:am:i6_15:.:INDEL:hetalt	1/1:FP:am:i6_15:277.01:INDEL:homalt	Yes	No																															3:136009513	136290671
PacBio_gatk4	gatk4hc_HG002_15kb_20kb_53X_SequelII.vcf.gz	GRCh38	small-variants	INDEL	3	chr3	136009513	136290671	44440	FN	G	GTTTTTTTTTT,GTTTTTTTTTTT	GT:BD:BK:BI:BVT:BLT:QQ	1|2:FN:.:i6_15:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:0	yes	no								skip																								136009513
DNAnexus	hs37d5_HG002_WGS_union.vcf.gz	GRCh37	small-variants	INDEL	3	chr3	136053953	136335111	59987862	FN	G	GCCC	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:lm:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	unsure	no	Compiled haplotype 1 and Illumina data shown such insertion; However, 10X genomics and ONT read didn't show such insertion. ONT reads shown complicated possibilities of different types of insertions/deletions aroudn this area.	unsure	no	benchmark may be correct in long C homopolymer, but all techs are somewhat noisy																											3:136053953	136335111
NCBI	HG002_grch38_dipcall.vcf.gz	GRCh38	small-variants	INDEL	3	chr3	196049844	196322973	-195953815	FP_FN	CAA	C	GT:BD:BK:QQ:BI:BVT:BLT	1|0:FN:am:.:d1_5:INDEL:het	1/1:FP:am:30:d1_5:INDEL:homalt	yes	no	evidence for HET							skip																								196049844
Common		GRCh37			4	chr4	362947	369158	0	FP	TAC	T	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:.:d1_5:INDEL:het	CommonFP			no	yes	hifiasm misses haplotype in diTR due to homozygous region													.:.:.:.:.:NOCALL:nocall	0/1:992.73:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:705.73:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:711.6:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:50:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:13:FP:.:d1_5:INDEL:het	4:362947	369158
Common		GRCh38			4	chr4	362947	369158	577	FP	TAC	T	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:.:d1_5:INDEL:het	CommonFP			no	yes	hifiasm misses haplotype in diTR due to homozygous region													.:.:.:.:.:NOCALL:nocall	0/1:992.73:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:739.73:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:258.6:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:50:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:13:FP:.:d1_5:INDEL:het		362947
Common		GRCh37			4	chr4	363524	369735	28	FN	G	GAT	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:lm:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no	yes	hifiasm miscalls ins size in adjacent diTR and homopolymer, likely due to noisy long homopolymer													0|1:FN:lm:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	4:363524	369735
Common		GRCh37			4	chr4	363552	369763	2	FN	TA	T	GT:BD:BK:QQ:BI:BVT:BLT	1|0:TP:gm:25.2288:d1_5:INDEL:het	0/1:TP:gm:25.2288:d1_5:INDEL:het	CommonFN			no	yes	hifiasm miscalls ins size in adjacent diTR and homopolymer, likely due to noisy long homopolymer													1|0:FN:lm:.:d1_5:INDEL:het	.:.:.:0:.:NOCALL:nocall	1|0:FN:lm:.:d1_5:INDEL:het	.:.:.:0:.:NOCALL:nocall	1|0:FN:lm:.:d1_5:INDEL:het	.:.:.:0:.:NOCALL:nocall	1|0:FN:lm:.:d1_5:INDEL:het	.:.:.:0:.:NOCALL:nocall	1|0:FN:lm:.:d1_5:INDEL:het	.:.:.:0:.:NOCALL:nocall	1|0:TP:gm:20.17:d1_5:INDEL:het	0/1:TP:gm:20.17:d1_5:INDEL:het	1|0:TP:gm:5:d1_5:INDEL:het	0/1:TP:gm:5:d1_5:INDEL:het	4:363552	369763
Common		GRCh37			4	chr4	363554	369765	1	FP	T	TATA	GT:QQ:BD:BK:BI:BVT:BLT	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	CommonFP			no	yes	hifiasm miscalls ins size in adjacent diTR and homopolymer, likely due to noisy long homopolymer													.:.:.:.:.:NOCALL:nocall	0/1:959.73:FP:lm:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:72.73:FP:lm:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:lm:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:350.07:FP:lm:i1_5:INDEL:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:4:FP:lm:i1_5:INDEL:het	4:363554	369765
Common		GRCh37			4	chr4	363555	369766	1	FN	T	A	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:lm:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no	yes	hifiasm miscalls ins size in adjacent diTR and homopolymer, likely due to noisy long homopolymer													0|1:FN:lm:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:959.73	0|1:FN:lm:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:72.73	0|1:FN:lm:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:30	0|1:FN:lm:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:350.07	0|1:FN:lm:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:4	4:363555	369766
Common		GRCh37			4	chr4	363556	369767	1	FP	T	A	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:27.6956:FP:lm:tv:SNP:het	CommonFP			no	yes	hifiasm miscalls ins size in adjacent diTR and homopolymer, likely due to noisy long homopolymer													.:.:.:.:.:NOCALL:nocall	0/1:1057.77:FP:lm:tv:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:81.77:FP:lm:tv:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:lm:tv:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:350.04:FP:lm:tv:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:14:FP:lm:tv:SNP:het	4:363556	369767
Common		GRCh37			4	chr4	363557	369768	1	FN	T	A	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:lm:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no	yes	hifiasm miscalls ins size in adjacent diTR and homopolymer, likely due to noisy long homopolymer													0|1:FN:lm:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	4:363557	369768
Common		GRCh37			4	chr4	363558	369769	289616	FP	T	A	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:lm:tv:SNP:het	CommonFP			no	yes	hifiasm miscalls ins size in adjacent diTR and homopolymer, likely due to noisy long homopolymer													.:.:.:.:.:NOCALL:nocall	0/1:1057.77:FP:lm:tv:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:81.77:FP:lm:tv:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:lm:tv:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:347.04:FP:lm:tv:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:11:FP:lm:tv:SNP:het	4:363558	369769
Common		GRCh37			4	chr4	653174	659385	0	FP_FN	C	CA	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:100:i1_5:INDEL:het	CommonFP_FN			no	yes	hifiasm misses haplotype in non-repeat due to homozygous region													1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:802.73:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:850.73:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:30:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:926.64:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:0:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:47.69:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:12:i1_5:INDEL:het	4:653174	659385
Common		GRCh38			4	chr4	653174	659385	190449	FP_FN	C	CA	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:100:i1_5:INDEL:het	CommonFP_FN			no	yes	hifiasm misses haplotype in non-repeat due to homozygous region													1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:802.73:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:853.73:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:30:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:555.64:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:0:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:47.69:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:12:i1_5:INDEL:het		653174
Common		GRCh37			4	chr4	843622	849834	171019	FP_FN	A	AC,ACC	GT:BD:BK:QQ:BI:BVT:BLT	2|2:FN:lm:.:i1_5:INDEL:homalt	1/1:FP:lm:100:i1_5:INDEL:homalt	CommonFP_FN			unsure	unsure	all techs noisy in C homopolymer													2|2:FN:lm:.:i1_5:INDEL:homalt	.:.:.:0:.:NOCALL:nocall	2|2:FN:lm:.:i1_5:INDEL:homalt	1/1:FP:lm:588.77:i1_5:INDEL:homalt	2|2:TP:gm:30:i1_5:INDEL:homalt	2/2:TP:gm:30:i1_5:INDEL:homalt	2|2:FN:lm:.:i1_5:INDEL:homalt	1/1:FP:lm:331.93:i1_5:INDEL:homalt	2|2:FN:lm:.:i1_5:INDEL:homalt	1/1:FP:lm:0:i1_5:INDEL:homalt	2|2:FN:lm:.:i1_5:INDEL:homalt	1/1:FP:lm:107.67:i1_5:INDEL:homalt	2|2:FN:lm:.:i1_5:INDEL:homalt	1/1:FP:lm:7:i1_5:INDEL:homalt	4:843622	849834
Common		GRCh37			4	chr4	1014641	1020853	63092	FN	CGGGGTGGGGACCCAGGCAGGGGATGGGGT	C	GT:BD:BK:BI:BVT:BLT:QQ	1|1:TP:gm:d16_plus:INDEL:homalt:100	1/1:TP:gm:d16_plus:INDEL:homalt:100	CommonFN			yes	no	hifiasm is well-supported by HiFi in long TR													1|1:TP:gm:d16_plus:INDEL:homalt:1087.73	1/1:TP:gm:d16_plus:INDEL:homalt:1087.73	1|1:FN:.:d16_plus:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:d16_plus:INDEL:homalt:30	1/1:TP:gm:d16_plus:INDEL:homalt:30	1|1:FN:.:d16_plus:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:d16_plus:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:lm:d16_plus:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:d16_plus:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	4:1014641	1020853
NYGC	HG-002-2x250-b37.recalibrated.haplotypeCalls.vcf.gz	GRCh37	small-variants	INDEL	4	chr4	1077733	1083945	19043	FP_FN	A	AT,ATTT	GT:BD:BK:BI:QQ:BVT:BLT	2|1:FN:am:i1_5:.:INDEL:hetalt	1/1:FP:am:i1_5:520.73:INDEL:homalt 	yes	no																															4:1077733	1083945
BCM-HGSC_xAtlas	HG002.GRCh38.60x.1_merged.vcf.gz	GRCh38	small-variants	INDEL	4	chr4	1096776	1102988	2360462	FP_FN	CAA	C,CA	GT:BD:BK:BI:QQ:BVT:BLT	1|2:FN:am:d1_5:.:INDEL:hetalt	1/1:FP:am:d1_5:13:INDEL:homalt 	Yes	No								skip																								1096776
Common		GRCh37			4	chr4	3465177	3463450	0	FP_FN	CGG	C,CGGG	GT:BD:BK:BI:QQ:BVT:BLT	1|2:FN:am:d1_5,i1_5:.:INDEL:hetalt	0/1:FP:am:d1_5:100:INDEL:het	CommonFP_FN			no	yes	likely hifiasm error in G homopolymer due to noisy HiFi reads													1|2:FN:am:d1_5,i1_5:.:INDEL:hetalt	0/1:FP:am:d1_5:459.86:INDEL:het	1|2:FN:am:d1_5,i1_5:.:INDEL:hetalt	0/1:FP:am:d1_5:433.73:INDEL:het	1|2:FN:am:d1_5,i1_5:.:INDEL:hetalt	0/1:FP:am:d1_5:30:INDEL:het	1|2:FN:.:d1_5,i1_5:.:INDEL:hetalt	.:.:.:.:0:NOCALL:nocall	1|2:FN:am:d1_5,i1_5:.:INDEL:hetalt	0/1:FP:am:d1_5:0:INDEL:het	1|2:FN:am:d1_5,i1_5:.:INDEL:hetalt	0/1:FP:am:d1_5:50:INDEL:het	1|2:FN:am:d1_5,i1_5:.:INDEL:hetalt	0/1:FP:am:d1_5:14:INDEL:het	4:3465177	3463450
Common		GRCh38			4	chr4	3465177	3463450	26957	FP_FN	CGG	C,CGGG	GT:BD:BK:BI:QQ:BVT:BLT	1|2:FN:am:d1_5,i1_5:.:INDEL:hetalt	0/1:FP:am:d1_5:100:INDEL:het	CommonFP_FN			no	yes	likely hifiasm error in G homopolymer due to noisy HiFi reads													1|2:FN:am:d1_5,i1_5:.:INDEL:hetalt	0/1:FP:am:d1_5:459.86:INDEL:het	1|2:FN:am:d1_5,i1_5:.:INDEL:hetalt	0/1:FP:am:d1_5:433.73:INDEL:het	1|2:FN:am:d1_5,i1_5:.:INDEL:hetalt	0/1:FP:am:d1_5:30:INDEL:het	1|2:FN:am:d1_5,i1_5:.:INDEL:hetalt	0/1:FP:am:d1_5:240.6:INDEL:het	1|2:FN:am:d1_5,i1_5:.:INDEL:hetalt	0/1:FP:am:d1_5:0:INDEL:het	1|2:FN:am:d1_5,i1_5:.:INDEL:hetalt	0/1:FP:am:d1_5:50:INDEL:het	1|2:FN:am:d1_5,i1_5:.:INDEL:hetalt	0/1:FP:am:d1_5:14:INDEL:het		3465177
Common		GRCh37			4	chr4	3492134	3490407	66103570	FN	A	AC	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:lm:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	benchmark appears coorect though C homopolymer in long TR													1|0:TP:gm:i1_5:INDEL:het:232.73	0/1:TP:gm:i1_5:INDEL:het:232.73	1|0:FN:lm:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	1|0:FN:lm:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:i1_5:INDEL:het:50	0/1:TP:gm:i1_5:INDEL:het:50	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	4:3492134	3490407
DNAnexus	hs37d5_HG002_WGS_union.vcf.gz	GRCh37	small-variants	SNP	4	chr4	70459695	69593977	117051389	FP	G	T	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:lm:tv:SNP:het	yes	no																															4:70459695	69593977
NYGC	HG-002-2x250-b37.recalibrated.haplotypeCalls.vcf.gz	GRCh37	small-variants	INDEL	4	chr4	187566520	186645366	0	FN	CATATATATATAT	C	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:.:d6_15:INDEL:het:.	.:.:.:.:NOCALL:nocall:0 	yes	no		no	unsure	benchmark has wrong del sizes in long TR due to HiFi noise																											4:187566520	186645366
Common		GRCh37			4	chr4	187566520	186645366	0	FP	CATATATATAT	CATATAT,C	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/2:100:FP:lm:d6_15:INDEL:het	CommonFP			no		benchmark has wrong del sizes in long TR due to HiFi noise													./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	1/1:30:FP:lm:d1_5:INDEL:homalt	.:.:.:.:.:NOCALL:nocall	0/2:899.06:FP:lm:d6_15:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/2:0:FP:lm:d6_15:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/2:69.51:FP:lm:d6_15:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:4:FP:lm:d1_5:INDEL:het	4:187566520	186645366
Common		GRCh37			4	chr4	187566520	186645366	18	FN	CATATATATATAT	C	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:lm:d6_15:INDEL:het:.	.:.:.:.:NOCALL:nocall:100	CommonFN			no		benchmark has wrong del sizes in long TR due to HiFi noise													0|1:TP:gm:d6_15:INDEL:het:322.73	0/1:TP:gm:d6_15:INDEL:het:322.73	0|1:FN:.:d6_15:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:d6_15:INDEL:het:.	.:.:.:.:NOCALL:nocall:30	0|1:FN:lm:d6_15:INDEL:het:.	.:.:.:.:NOCALL:nocall:899.06	0|1:FN:lm:d6_15:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:d6_15:INDEL:het:.	.:.:.:.:NOCALL:nocall:69.51	0|1:FN:lm:d6_15:INDEL:het:.	.:.:.:.:NOCALL:nocall:4	4:187566520	186645366
Common		GRCh37			4	chr4	187566538	186645384	1342	FN	TATATA	T	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:lm:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no		benchmark has wrong del sizes in long TR due to HiFi noise													1|0:FN:lm:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:lm:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:lm:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:lm:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:lm:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:lm:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	4:187566538	186645384
BCM-HGSC_xAtlas	HG002.GRCh38.60x.1_merged.vcf.gz	GRCh38	small-variants	INDEL	4	chr4	187567880	186646726	35800	FP_FN	GAA	G,GA	GT:BD:BK:BI:QQ:BVT:BLT	2|1:FN:am:d1_5:.:INDEL:hetalt	1/1:FP:am:d1_5:18:INDEL:homalt 	Yes	No								skip																								187567880
Common		GRCh37			4	chr4	187603680	186682526	0	FP_FN	CAAAAAAA	C,CAAAAAAAAAAAAAAAAAAAAA	GT:BD:BK:BI:QQ:BVT:BLT	1|2:TP:gm:d6_15,i6_15:100:INDEL:hetalt	0/1:TP:gm:d6_15:100:INDEL:het	CommonFP_FN			yes	no	Despite long homopolymer, hifiasm appears correct since it's supported by illumina and average of reads on each HiFi haplotype													1|2:FN:am:d6_15,i6_15:.:INDEL:hetalt	1/1:FP:am:d6_15:2369.73:INDEL:homalt	1|2:FN:am:d6_15,i6_15:.:INDEL:hetalt	1/1:FP:am:d6_15:1096.73:INDEL:homalt	1|2:FN:am:d6_15,i6_15:.:INDEL:hetalt	1/1:FP:am:d6_15:30:INDEL:homalt	1|2:FN:am:d6_15,i6_15:.:INDEL:hetalt	1/1:FP:am:d6_15:1256.01:INDEL:homalt	1|2:FN:am:d6_15,i6_15:.:INDEL:hetalt	1/1:FP:am:d6_15:0:INDEL:homalt	1|2:TP:gm:d6_15,i6_15:378.92:INDEL:hetalt	0/1:TP:gm:d6_15:378.92:INDEL:het	1|2:FN:am:d6_15,i6_15:.:INDEL:hetalt	1/1:FP:am:d6_15:12:INDEL:homalt	4:187603680	186682526
NYGC	HG-002-2x250-b38.recalibrated.haplotypeCalls.vcf.gz	GRCh38	small-variants	INDEL	4	chr4	187603680	186682526	0	FP_FN	CAAAAAAA	C,CAAAAAAAAAAAAAAAAAAAAA	GT:BD:BK:BI:QQ:BVT:BLT	1|2:FN:am:d6_15,i6_15:.:INDEL:hetalt	1/1:FP:am:d6_15:1087.73:INDEL:homalt 	yes	yes		yes	no	Despite long homopolymer, hifiasm appears correct since it's supported by illumina and average of reads on each HiFi haplotype																												187603680
Common		GRCh38			4	chr4	187603680	186682526	6127	FP_FN	CAAAAAAA	C,CAAAAAAAAAAAAAAAAAAAAA	GT:BD:BK:QQ:BI:BVT:BLT	1|2:TP:gm:100:d6_15,i6_15:INDEL:hetalt	0/1:TP:gm:100:d6_15:INDEL:het	CommonFP_FN			yes	no	Despite long homopolymer, hifiasm appears correct since it's supported by illumina and average of reads on each HiFi haplotype													1|2:FN:am:.:d6_15,i6_15:INDEL:hetalt	1/1:FP:am:2369.73:d6_15:INDEL:homalt	1|2:FN:am:.:d6_15,i6_15:INDEL:hetalt	1/1:FP:am:1087.73:d6_15:INDEL:homalt	1|2:FN:am:.:d6_15,i6_15:INDEL:hetalt	1/1:FP:am:30:d6_15:INDEL:homalt	1|2:FN:am:.:d6_15,i6_15:INDEL:hetalt	0/1:FP:am:612.06:d6_15:INDEL:het	1|2:FN:am:.:d6_15,i6_15:INDEL:hetalt	1/1:FP:am:0:d6_15:INDEL:homalt	1|2:TP:gm:378.92:d6_15,i6_15:INDEL:hetalt	0/1:TP:gm:378.92:d6_15:INDEL:het	1|2:FN:am:.:d6_15,i6_15:INDEL:hetalt	1/1:FP:am:12:d6_15:INDEL:homalt		187603680
Common		GRCh37			4	chr4	187609807	186688653	7107	FN	GC	GCC,*	GT:BD:BK:BI:BVT:BLT:QQ	2|1:FN:lm:i1_5:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no	yes	hifiasm has extra ins due to noisy C homopolymer													2|1:FN:lm:i1_5:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:0	2|1:FN:lm:i1_5:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:0	2|1:FN:lm:i1_5:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:0	2|1:FN:lm:i1_5:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:0	2|1:FN:lm:i1_5:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:0	2|1:FN:lm:i1_5:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:0	2|1:FN:lm:i1_5:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:0	4:187609807	186688653
BCM-HGSC_xAtlas	HG002.hs37d5.60x.1_merged.vcf.gz	GRCh37	small-variants	INDEL	4	chr4	187616914	186695760	9346	FP_FN	A	AAC	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:18:i1_5:INDEL:het 	Yes	No																															4:187616914	186695760
Common		GRCh37			4	chr4	187626260	186705106	0	FN	A	AT	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no	yes	likely hifiasm error in long homopolymer due to noisy HiFi reads													0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	4:187626260	186705106
Common		GRCh38			4	chr4	187626260	186705106	-185293366	FN	A	AT	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no	yes	likely hifiasm error in long homopolymer due to noisy HiFi reads													0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0		187626260
PacBio_gatk4	gatk4hc_HG002_15kb_20kb_53X_SequelII.vcf.gz	GRCh38	small-variants	INDEL	5	chr5	1411855	1411740	3774	FN	GCACATACCATGCAACATACACACTCAGACA	G	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:.:d16_plus:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	yes	no								skip																								1411855
ITER	ITERteam_small-variation_GRCh38_ILMN-PB-ONT.vcf.gz	GRCh38	small-variants	SNP	5	chr5	1415629	1415514	12382	FN	A	T	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	Yes	No	All technologies in truth called this variant. Low MQ in query.							skip																								1415629
ITER	ITERteam_small-variation_GRCh38_ILMN-PB-ONT.vcf.gz	GRCh38	small-variants	SNP	5	chr5	1428011	1427896	67996696	FN	C	T	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	Yes	No	All technologies in truth called this variant. Low MQ in query.							skip																								1428011
ITER	ITERteam_small-variation_GRCh38_ILMN-PB-ONT.vcf.gz	GRCh38	small-variants	SNP	5	chr5	68720419	69424592	19417	FP_FN	T	G	GT:BD:BK:QQ:BI:BVT:BLT	0|1:FN:am:.:tv:SNP:het	1/1:FP:am:205.58:tv:SNP:homalt	Yes	No	Het genotype well supported by all technologies in truth. Query reads have low MQ and fewer reads in comparison to truth.							skip																								68720419
Common		GRCh37			5	chr5	68739836	69444009	0	FP_FN	T	TAAAAAAAAAAAAA,TAAAAAAAAAAAAAAAAAAAAAAAAAA,TAAAAAAAAAAAAAAAAAAA,TAAAAAAAAAAAAAA	GT:BD:BK:BI:QQ:BVT:BLT	2|1:FN:am:i16_plus,i6_15:.:INDEL:hetalt	4/1:FP:am:i6_15:100:INDEL:hetalt	CommonFP_FN			unsure	unsure	hifiasm may be correct but ~26bp ins on one haplotype in homopolymer, so uncertain													2|1:TP:gm:i16_plus,i6_15:1432.73:INDEL:hetalt	2/1:TP:gm:i16_plus,i6_15:1432.73:INDEL:hetalt	2|1:FN:am:i16_plus,i6_15:.:INDEL:hetalt	2/2:FP:am:i16_plus:391.73:INDEL:homalt	2|1:FN:lm:i16_plus,i6_15:.:INDEL:hetalt	3/3:FP:lm:i16_plus:30:INDEL:homalt	2|1:FN:am:i16_plus,i6_15:.:INDEL:hetalt	1/1:FP:am:i6_15:467.06:INDEL:homalt	2|1:FN:lm:i16_plus,i6_15:.:INDEL:hetalt	.:.:.:.:0:NOCALL:nocall	2|1:TP:gm:i16_plus,i6_15:185.5:INDEL:hetalt	2/1:TP:gm:i16_plus,i6_15:185.5:INDEL:hetalt	2|1:FN:am:i16_plus,i6_15:.:INDEL:hetalt	1/1:FP:am:i6_15:10:INDEL:homalt	5:68739836	69444009
Common		GRCh38			5	chr5	68739836	69444009	1483599	FP_FN	T	TAAAAAAAAAAAAA,TAAAAAAAAAAAAAA,TAAAAAAAAAAAAAAAAAAAAAAAAAA,TAAAAAAAAAAAAAAAAAAA,TAAAAAAAAA	GT:BD:BK:BI:QQ:BVT:BLT	3|1:FN:am:i16_plus,i6_15:.:INDEL:hetalt	2/1:FP:am:i6_15:100:INDEL:hetalt	CommonFP_FN			unsure	unsure	hifiasm may be correct but ~26bp ins on one haplotype in homopolymer, so uncertain													3|1:TP:gm:i16_plus,i6_15:1432.73:INDEL:hetalt	3/1:TP:gm:i16_plus,i6_15:1432.73:INDEL:hetalt	3|1:FN:am:i16_plus,i6_15:.:INDEL:hetalt	3/3:FP:am:i16_plus:391.73:INDEL:homalt	3|1:FN:lm:i16_plus,i6_15:.:INDEL:hetalt	4/4:FP:lm:i16_plus:30:INDEL:homalt	3|1:FN:lm:i16_plus,i6_15:.:INDEL:hetalt	0/5:FP:lm:i6_15:13.2:INDEL:het	3|1:FN:lm:i16_plus,i6_15:.:INDEL:hetalt	.:.:.:.:0:NOCALL:nocall	3|1:TP:gm:i16_plus,i6_15:185.5:INDEL:hetalt	3/1:TP:gm:i16_plus,i6_15:185.5:INDEL:hetalt	3|1:FN:am:i16_plus,i6_15:.:INDEL:hetalt	1/1:FP:am:i6_15:11:INDEL:homalt		68739836
Common		GRCh37			5	chr5	70223435	70927608	0	FN	CA	C	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:.:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	CommonFN			unsure	unsure	Probably correct but long homopolymer in region of SMN1 that has little read mapping, and only reads from one 10x haplotype, so hard to confirm if GT is correct													1|1:FN:.:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:d1_5:INDEL:homalt:30	1/1:TP:gm:d1_5:INDEL:homalt:30	1|1:FN:.:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	5:70223435	70927608
Common		GRCh38			5	chr5	70223435	70927608	1436	FN	CA	C	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:.:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	CommonFN			unsure	unsure	Probably correct but long homopolymer in region of SMN1 that has little read mapping, and only reads from one 10x haplotype, so hard to confirm if GT is correct													1|1:FN:.:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:d1_5:INDEL:homalt:30	1/1:TP:gm:d1_5:INDEL:homalt:30	1|1:FN:.:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0		70223435
Common		GRCh37			5	chr5	70224871	70929044	0	FN	C	T	GT:BD:BK:BI:BVT:BLT:QQ	0|1:TP:gm:ti:SNP:het:21.1978	0/1:TP:gm:ti:SNP:het:21.1978	CommonFN			yes	no	Variants in hifiasm assembly of SMN1 are supported by ONT and 10x, so likely to be accurate													0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	5:70224871	70929044
Common		GRCh38			5	chr5	70224871	70929044	2029	FN	C	T	GT:BD:BK:QQ:BI:BVT:BLT	0|1:TP:gm:22.1479:ti:SNP:het	0/1:TP:gm:22.1479:ti:SNP:het	CommonFN			yes	no	Variants in hifiasm assembly of SMN1 are supported by ONT and 10x, so likely to be accurate													0|1:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall		70224871
Roche	RN_HG002_Illumina_PacBio_Oxford_GRCh37.vcf.gz	GRCh37	small-variants	SNP	5	chr5	70226900	70931073	3497	FP	A	C	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:23.6692:FP:.:tv:SNP:het 	yes	no																															5:70226900	70931073
Common		GRCh37			5	chr5	70230397	70934570	0	FN	A	G	GT:BD:BK:BI:BVT:BLT:QQ	1|1:TP:gm:ti:SNP:homalt:100	1/1:TP:gm:ti:SNP:homalt:100	CommonFN			yes	no	Variants in hifiasm assembly of SMN1 are supported by ONT and 10x, so likely to be accurate													1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:ti:SNP:homalt:11	1/1:TP:gm:ti:SNP:homalt:11	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	5:70230397	70934570
Common		GRCh38			5	chr5	70230397	70934570	1581	FN	A	G	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:100:ti:SNP:homalt	1/1:TP:gm:100:ti:SNP:homalt	CommonFN			yes	no	Variants in hifiasm assembly of SMN1 are supported by ONT and 10x, so likely to be accurate													1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall		70230397
Common		GRCh37			5	chr5	70231978	70936151	691	FN	C	CTTTTTT	GT:BD:BK:BI:BVT:BLT:QQ	1|1:TP:gm:i6_15:INDEL:homalt:100	1/1:TP:gm:i6_15:INDEL:homalt:100	CommonFN			yes		hifiasm supported by Illumina in ins in long homopolymer													1|1:FN:.:i6_15:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:i6_15:INDEL:homalt:52.7	1/1:TP:gm:i6_15:INDEL:homalt:52.7	1|1:FN:.:i6_15:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:i6_15:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:i6_15:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:i6_15:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:i6_15:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	5:70231978	70936151
Roche	RN_HG002_Illumina_PacBio_Oxford.vcf.gz	GRCh38	small-variants	SNP	5	chr5	70232669	70936842	1360	FP_FN	C	G	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:tv:SNP:homalt	0/1:FP:am:39.9993:tv:SNP:het 	yes	no		yes	no	Variants in hifiasm assembly of SMN1 are supported by ONT and 10x, so likely to be accurate				skip																								70232669
Common		GRCh37			5	chr5	70234029	70938202	0	FN	A	G	GT:BD:BK:BI:BVT:BLT:QQ	1|1:TP:gm:ti:SNP:homalt:100	1/1:TP:gm:ti:SNP:homalt:100	CommonFN			yes	no	Variants in hifiasm assembly of SMN1 are supported by ONT and 10x, so likely to be accurate													1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:ti:SNP:homalt:30	1/1:TP:gm:ti:SNP:homalt:30	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	5:70234029	70938202
Common		GRCh38			5	chr5	70234029	70938202	4344	FN	A	G	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:100:ti:SNP:homalt	1/1:TP:gm:100:ti:SNP:homalt	CommonFN			yes	no	Variants in hifiasm assembly of SMN1 are supported by ONT and 10x, so likely to be accurate													1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:TP:gm:30:ti:SNP:homalt	1/1:TP:gm:30:ti:SNP:homalt	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall		70234029
Common		GRCh37			5	chr5	70238373	70942546	0	FN	A	G	GT:BD:BK:BI:BVT:BLT:QQ	1|1:TP:gm:ti:SNP:homalt:21.0316	1/1:TP:gm:ti:SNP:homalt:21.0316	CommonFN			yes	no	Variants in hifiasm assembly of SMN1 are supported by ONT and 10x, so likely to be accurate													1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:ti:SNP:homalt:30	1/1:TP:gm:ti:SNP:homalt:30	1|1:TP:gm:ti:SNP:homalt:13.3	1/1:TP:gm:ti:SNP:homalt:13.3	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	5:70238373	70942546
Common		GRCh38			5	chr5	70238373	70942546	3025	FN	A	G	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:30.97:ti:SNP:homalt	1/1:TP:gm:30.97:ti:SNP:homalt	CommonFN			yes	no	Variants in hifiasm assembly of SMN1 are supported by ONT and 10x, so likely to be accurate													1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:TP:gm:30:ti:SNP:homalt	1/1:TP:gm:30:ti:SNP:homalt	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall		70238373
Common		GRCh37			5	chr5	70241398	70945571	0	FN	CTG	C	GT:BD:BK:BI:BVT:BLT:QQ	1|1:TP:gm:d1_5:INDEL:homalt:33.0103	1/1:TP:gm:d1_5:INDEL:homalt:33.0103	CommonFN			yes	no	Variants in hifiasm assembly of SMN1 are supported by ONT and 10x, so likely to be accurate													1|1:FN:.:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	5:70241398	70945571
Common		GRCh38			5	chr5	70241398	70945571	1037	FN	CTG	C	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:15.3466:d1_5:INDEL:homalt	1/1:TP:gm:15.3466:d1_5:INDEL:homalt	CommonFN			yes	no	Variants in hifiasm assembly of SMN1 are supported by ONT and 10x, so likely to be accurate													1|1:FN:.:.:d1_5:INDEL:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:d1_5:INDEL:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:d1_5:INDEL:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:d1_5:INDEL:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:d1_5:INDEL:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:d1_5:INDEL:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:d1_5:INDEL:homalt	.:.:.:0:.:NOCALL:nocall		70241398
Common		GRCh37			5	chr5	70242435	70946608	0	FN	T	C	GT:BD:BK:BI:BVT:BLT:QQ	1|1:TP:gm:ti:SNP:homalt:39.9993	1/1:TP:gm:ti:SNP:homalt:39.9993	CommonFN			yes	no	Variants in hifiasm assembly of SMN1 are supported by ONT and 10x, so likely to be accurate													1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:ti:SNP:homalt:30	1/1:TP:gm:ti:SNP:homalt:30	1|1:TP:gm:ti:SNP:homalt:13.8	1/1:TP:gm:ti:SNP:homalt:13.8	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	5:70242435	70946608
Common		GRCh38			5	chr5	70242435	70946608	543	FN	T	C	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:100:ti:SNP:homalt	1/1:TP:gm:100:ti:SNP:homalt	CommonFN			yes	no	Variants in hifiasm assembly of SMN1 are supported by ONT and 10x, so likely to be accurate													1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:TP:gm:30:ti:SNP:homalt	1/1:TP:gm:30:ti:SNP:homalt	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall		70242435
Common		GRCh37			5	chr5	70242978	70947151	0	FN	A	G	GT:BD:BK:BI:BVT:BLT:QQ	1|1:TP:gm:ti:SNP:homalt:100	1/1:TP:gm:ti:SNP:homalt:100	CommonFN			yes	no	Variants in hifiasm assembly of SMN1 are supported by ONT and 10x, so likely to be accurate													1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:ti:SNP:homalt:30	1/1:TP:gm:ti:SNP:homalt:30	1|1:TP:gm:ti:SNP:homalt:17.3	1/1:TP:gm:ti:SNP:homalt:17.3	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	5:70242978	70947151
Common		GRCh38			5	chr5	70242978	70947151	6124	FN	A	G	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:100:ti:SNP:homalt	1/1:TP:gm:100:ti:SNP:homalt	CommonFN			yes	no	Variants in hifiasm assembly of SMN1 are supported by ONT and 10x, so likely to be accurate													1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:TP:gm:30:ti:SNP:homalt	1/1:TP:gm:30:ti:SNP:homalt	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall		70242978
Common		GRCh38			5	chr5	70249102	70953275	24511649	FN	G	C	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:100:tv:SNP:homalt	1/1:TP:gm:100:tv:SNP:homalt	CommonFN			yes	no	Variants in hifiasm assembly of SMN1 are supported by ONT and 10x, so likely to be accurate													1|1:TP:gm:235.77:tv:SNP:homalt	1/1:TP:gm:235.77:tv:SNP:homalt	1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:TP:gm:30:tv:SNP:homalt	1/1:TP:gm:30:tv:SNP:homalt	1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall		70249102
Common		GRCh37			5	chr5	94800628	95464924	0	FN	C	CT	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no	yes	likely hifiasm error in long homopolymer due to noisy HiFi reads													0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	5:94800628	95464924
Common		GRCh38			5	chr5	94800628	95464924	85544	FN	C	CT	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no	yes	likely hifiasm error in long homopolymer due to noisy HiFi reads													0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0		94800628
Roche	RN_HG002_Illumina_PacBio_Oxford_GRCh37.vcf.gz	GRCh37	small-variants	INDEL	5	chr5	94886172	95550468	0	FP	TA	T	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:.:d1_5:INDEL:het 	no	yes	seems real variant from ILM which is more accurate for homopolymer INDELs, also supported in PB	no	yes	hifiasm misses del in homopolymer due to region of homozygosity																											5:94886172	95550468
Common		GRCh37			5	chr5	94886172	95550468	0	FP	TA	T	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:.:d1_5:INDEL:het	CommonFP			no	yes	hifiasm misses del in homopolymer due to region of homozygosity													.:.:.:.:.:NOCALL:nocall	0/1:201.73:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:306.73:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:451.6:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:20.82:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:13:FP:.:d1_5:INDEL:het	5:94886172	95550468
Common		GRCh38			5	chr5	94886172	95550468	1578197	FP	TA	T	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:.:d1_5:INDEL:het	CommonFP			no	yes	hifiasm misses del in homopolymer due to region of homozygosity													.:.:.:.:.:NOCALL:nocall	0/1:201.73:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:294.73:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:93.6:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:20.79:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:13:FP:.:d1_5:INDEL:het		94886172
Common		GRCh37			5	chr5	96464369	97128665	0	FP	C	CA	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:.:i1_5:INDEL:het	CommonFP			no	yes	hifiasm misses ins in homopolymer due to region of homozygosity													.:.:.:.:.:NOCALL:nocall	0/1:533.73:FP:.:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:423.73:FP:.:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:.:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:562.64:FP:.:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:.:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:50:FP:.:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:14:FP:.:i1_5:INDEL:het	5:96464369	97128665
Roche	RN_HG002_Illumina_PacBio_Oxford.vcf.gz	GRCh38	small-variants	INDEL	5	chr5	96464369	97128665	0	FP	C	CA	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:.:i1_5:INDEL:het 	unsure	unsure	seems correct in ILM/PB/10x	no	yes	hifiasm misses ins in homopolymer due to region of homozygosity																												96464369
NYGC	HG-002-2x250-b38.recalibrated.haplotypeCalls.vcf.gz	GRCh38	small-variants	INDEL	5	chr5	96464369	97128665	0	FP	C	CA	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:420.73:FP:.:i1_5:INDEL:het 	no	yes	There is evidence of this insertion in all sequencing techs. Not sure why this doesn't appear in their call set.	no	yes	hifiasm misses ins in homopolymer due to region of homozygosity																												96464369
Common		GRCh38			5	chr5	96464369	97128665	37489270	FP	C	CA	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:.:i1_5:INDEL:het	CommonFP			no	yes	hifiasm misses ins in homopolymer due to region of homozygosity													.:.:.:.:.:NOCALL:nocall	0/1:533.73:FP:.:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:420.73:FP:.:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:.:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:328.64:FP:.:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:.:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:50:FP:.:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:14:FP:.:i1_5:INDEL:het		96464369
Common		GRCh37			5	chr5	133953625	134617935	0	FN	ATTTCACCATGATCATTTT	A	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:d16_plus:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no	yes	consensus error in hifiasm													1|0:FN:.:d16_plus:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d16_plus:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d16_plus:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d16_plus:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d16_plus:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d16_plus:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d16_plus:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	5:133953625	134617935
PacBio_gatk4	gatk4hc_HG002_15kb_20kb_53X_SequelII.vcf.gz	GRCh38	small-variants	INDEL	5	chr5	133953625	134617935	0	FN	ATTTCACCATGATCATTTT	A	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:d16_plus:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	no	yes	https://github.com/chhylp123/hifiasm/issues/60#issuecomment-745113822	no	yes	consensus error in hifiasm																												133953625
Common		GRCh38			5	chr5	133953625	134617935	6690	FN	ATTTCACCATGATCATTTT	A	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:d16_plus:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no	yes	consensus error in hifiasm													1|0:FN:.:d16_plus:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d16_plus:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d16_plus:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d16_plus:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d16_plus:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d16_plus:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d16_plus:INDEL:het:.	.:.:.:.:NOCALL:nocall:0		133953625
Common		GRCh37			5	chr5	133960315	134624625	0	FP_FN	GT	G	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:100:d1_5:INDEL:het	CommonFP_FN			no	yes	hifiasm misses ref on one haplotype, likely due to region of homozygosity													1|1:FN:.:.:d1_5:INDEL:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:181.73:d1_5:INDEL:het	1|1:FN:.:.:d1_5:INDEL:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:130.6:d1_5:INDEL:het	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:0:d1_5:INDEL:het	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:48.9:d1_5:INDEL:het	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:5:d1_5:INDEL:het	5:133960315	134624625
NCBI	HG002_grch38_dipcall.vcf.gz	GRCh38	small-variants	INDEL	5	chr5	133960315	134624625	0	FN	GT	G	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:.:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	yes	no	DEL here, but evidence supports 2bps del too	no	yes	hifiasm misses ref on one haplotype, likely due to region of homozygosity				skip																								133960315
Common		GRCh38			5	chr5	133960315	134624625	3176	FP_FN	GT	G	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:100:d1_5:INDEL:het	CommonFP_FN			no	yes	hifiasm misses ref on one haplotype, likely due to region of homozygosity													1|1:FN:.:.:d1_5:INDEL:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:147.73:d1_5:INDEL:het	1|1:FN:.:.:d1_5:INDEL:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:62.6:d1_5:INDEL:het	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:0:d1_5:INDEL:het	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:48.86:d1_5:INDEL:het	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:5:d1_5:INDEL:het		133960315
PacBio_gatk4	gatk4hc_HG002_15kb_20kb_52X_SequelII.vcf.gz	GRCh37	small-variants	INDEL	5	chr5	133963491	134627801	0	FP	AAAAT	A	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:1894.73:FP:lm:d1_5:INDEL:het	no	yes	read support from multiple techs shows genotype is 4bp insertion / 4bp deletion	no	yes	hifiasm misses del on one haplotype and only calls ins, likely due to region of homozygosity																											5:133963491	134627801
CMH_DRAGEN_3.6.3	NA24385.hard-filtered.vcf.gz	GRCh37	small-variants	INDEL	5	chr5	133963491	134627801	0	FP	AAAAT	A	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:156.08:FP:lm:d1_5:INDEL:het	no	yes	In SINE/TR. Benchmark and query don't match records. The query is better supposed in almost all alignments	no	yes	hifiasm misses del on one haplotype and only calls ins, likely due to region of homozygosity																											5:133963491	134627801
Common		GRCh37			5	chr5	133963491	134627801	0	FP	AAAAT	A	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:lm:d1_5:INDEL:het	CommonFP			no	yes	hifiasm misses del on one haplotype and only calls ins, likely due to region of homozygosity													.:.:.:.:.:NOCALL:nocall	0/1:1894.73:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:1295.73:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:1183.06:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:156.08:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:8:FP:lm:d1_5:INDEL:het	5:133963491	134627801
Common		GRCh37			5	chr5	133963491	134627801	0	FN	A	AAAAT	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:am:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no	yes	hifiasm misses del on one haplotype and only calls ins, likely due to region of homozygosity													1|1:FN:am:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:am:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:am:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:am:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:am:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:am:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:lm:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	5:133963491	134627801
BCM-HGSC_xAtlas	HG002.GRCh38.60x.1_merged.vcf.gz	GRCh38	small-variants	INDEL	5	chr5	133963491	134627801	0	FP	AAAAT	A	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:8:FP:lm:d1_5:INDEL:het 	Unsure	No	Illumina 60x, 10X phased and PacBio Sequel II suggest possible AAAAT->A,AAAATAAAT at chr5:134627801.	no	yes	hifiasm misses del on one haplotype and only calls ins, likely due to region of homozygosity																												133963491
Common		GRCh38			5	chr5	133963491	134627801	0	FN	A	AAAAT	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:am:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no	yes	hifiasm misses del on one haplotype and only calls ins, likely due to region of homozygosity													1|1:FN:am:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:am:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:am:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:am:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:am:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:am:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:lm:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0		133963491
Common		GRCh38			5	chr5	133963491	134627801	4	FP	AAAAT	A	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:lm:d1_5:INDEL:het	CommonFP			no	yes	hifiasm misses del on one haplotype and only calls ins, likely due to region of homozygosity													.:.:.:.:.:NOCALL:nocall	0/1:1894.73:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:1180.73:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:474.06:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:157.68:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:8:FP:lm:d1_5:INDEL:het		133963491
Common		GRCh37			5	chr5	133963495	134627805	0	FP	T	TAAAT	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:am:i1_5:INDEL:het	CommonFP			no	yes	hifiasm misses del on one haplotype and only calls ins, likely due to region of homozygosity													.:.:.:.:.:NOCALL:nocall	0/1:1894.73:FP:am:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:1295.73:FP:am:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:am:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:1183.06:FP:am:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:am:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:156.08:FP:am:i1_5:INDEL:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	5:133963495	134627805
DNAnexus	GRCh38_HG002_WGS_union.vcf.gz	GRCh38	small-variants	INDEL	5	chr5	133963495	134627805	0	FP	T	TAAAT	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:am:i1_5:INDEL:het 	yes	yes	Both benchmark set and query callset are right. The differences is due to VCF variant record formatting. Also, this variant is presented in the query callset at chr5:134627801, rather than at chr5:134627805	no	yes	hifiasm misses del on one haplotype and only calls ins, likely due to region of homozygosity																												133963495
Common		GRCh38			5	chr5	133963495	134627805	523	FP	T	TAAAT	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:am:i1_5:INDEL:het	CommonFP			no	yes	hifiasm misses del on one haplotype and only calls ins, likely due to region of homozygosity													.:.:.:.:.:NOCALL:nocall	0/1:1894.73:FP:am:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:1180.73:FP:am:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:am:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:474.06:FP:am:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:am:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:157.68:FP:am:i1_5:INDEL:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.		133963495
Common		GRCh37			5	chr5	133964018	134628328	0	FP_FN	T	TA	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:100:i1_5:INDEL:het	CommonFP_FN			no	yes	hifiasm misses ref on one haplotype, likely due to region of moderate homozygosity													1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:350.73:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:593.73:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:30:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:648.64:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:0:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:50:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:16:i1_5:INDEL:het	5:133964018	134628328
Common		GRCh38			5	chr5	133964018	134628328	3251330	FP_FN	T	TA	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:100:i1_5:INDEL:het	CommonFP_FN			no	yes	hifiasm misses ref on one haplotype, likely due to region of moderate homozygosity													1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:350.73:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:593.73:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:30:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:181.64:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:0:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:50:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:16:i1_5:INDEL:het		133964018
DNAnexus	GRCh38_HG002_WGS_union.vcf.gz	GRCh38	small-variants	SNP	5	chr5	137215347	137879658	16	FP	G	T	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:.:tv:SNP:het 	yes	no	ONT - 4 DEL/1 INS 							skip																								137215347
DNAnexus	hs37d5_HG002_WGS_union.vcf.gz	GRCh37	small-variants	SNP	5	chr5	137215363	137879674	3063583	FP	G	T	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:.:tv:SNP:het	yes	no																															5:137215363	137879674
ITER	ITERteam_small-variation_GRCh37_ILMN-PB-ONT.vcf.gz	GRCh37	small-variants	INDEL	5	chr5	140322842	140943257	39669511	FP_FN	C	CA,CAA	GT:BD:BK:QQ:BI:BVT:BLT	0|2:FN:lm:.:i1_5:INDEL:het	0/1:FP:lm:105.64:i1_5:INDEL:het	Yes	No																															5:140322842	140943257
Common		GRCh37			5	chr5	180039768	180612768	0	FN	GC	G	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no	yes	look likely to be hifiasm consensus error since they all come from one HiFi read and aren't supported by illumina.													1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	5:180039768	180612768
Common		GRCh38			5	chr5	180039768	180612768	326	FN	GC	G	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no	yes	look likely to be hifiasm consensus error since they all come from one HiFi read and aren't supported by illumina.													1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0		180039768
Common		GRCh37			5	chr5	180040094	180613094	0	FN	AG	A	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no	yes	look likely to be hifiasm consensus error since they all come from one HiFi read and aren't supported by illumina.													1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	5:180040094	180613094
NYGC	HG-002-2x250-b38.recalibrated.haplotypeCalls.vcf.gz	GRCh38	small-variants	INDEL	5	chr5	180040094	180613094	0	FN	AG	A	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0 	unsure		this appears to only be in the ONT data and is part of a small G homoploymer run	no	yes	look likely to be hifiasm consensus error since they all come from one HiFi read and aren't supported by illumina.						I don't see evidence of deletion, appears to be HOM_REF																						180040094
Common		GRCh38			5	chr5	180040094	180613094	71	FN	AG	A	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no	yes	look likely to be hifiasm consensus error since they all come from one HiFi read and aren't supported by illumina.													1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0		180040094
Common		GRCh37			5	chr5	180040165	180613165	0	FN	GC	G	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no	yes	look likely to be hifiasm consensus error since they all come from one HiFi read and aren't supported by illumina.													1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	5:180040165	180613165
Common		GRCh38			5	chr5	180040165	180613165	-72714909	FN	GC	G	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no	yes	look likely to be hifiasm consensus error since they all come from one HiFi read and aren't supported by illumina.													1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0		180040165
PacBio_gatk4	gatk4hc_HG002_15kb_20kb_52X_SequelII.vcf.gz	GRCh37	small-variants	INDEL	6	chr6	108219460	107898256	16978	FP_FN	CA	C	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:719.73:d1_5:INDEL:het	yes	no																															6:108219460	107898256
PacBio_gatk4	gatk4hc_HG002_15kb_20kb_53X_SequelII.vcf.gz	GRCh38	small-variants	SNP	6	chr6	108236438	107915234	6677	FP_FN	G	T	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:tv:SNP:homalt	0/1:FP:am:1229.77:tv:SNP:het	yes	no								skip																								108236438
PacBio_gatk4	gatk4hc_HG002_15kb_20kb_52X_SequelII.vcf.gz	GRCh37	small-variants	INDEL	6	chr6	108243115	107921911	41834442	FP	T	TGGG	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	1/1:2262.73:FP:am:i1_5:INDEL:homalt	unsure	unsure	nearly equivalent representation of a complex event, but this borders a HP so hard to interpret	yes	no	supported by all techs, though different representation in Illumina																											6:108243115	107921911
PacBio_gatk4	gatk4hc_HG002_15kb_20kb_52X_SequelII.vcf.gz	GRCh37	small-variants	INDEL	6	chr6	150077489	149756353	1832	FP_FN	C	CT	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:579.73:i1_5:INDEL:het	yes	no																															6:150077489	149756353
Common		GRCh37			6	chr6	150079321	149758185	10432	FP	A	ATT	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	1/1:9.1656:FP:am:i1_5:INDEL:homalt	CommonFP			unsure		noisy extremely long imperfect homopolymer due to long ins													.:.:.:.:.:NOCALL:nocall	1/1:1147.73:FP:lm:i1_5:INDEL:homalt	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	1/1:0:FP:lm:i1_5:INDEL:homalt	.:.:.:.:.:NOCALL:nocall	0/1:52.2:FP:am:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:17:FP:lm:i1_5:INDEL:het	6:150079321	149758185
Common		GRCh37			6	chr6	150089753	149768617	0	FN	G	GT	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no	yes	likely hifiasm error in homopolymer due to noisy HiFi													1|0:TP:gm:i1_5:INDEL:het:26.74	0/1:TP:gm:i1_5:INDEL:het:26.74	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	6:150089753	149768617
Common		GRCh38			6	chr6	150089753	149768617	11725	FN	G	GT	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no	yes	likely hifiasm error in homopolymer due to noisy HiFi													1|0:TP:gm:i1_5:INDEL:het:26.74	0/1:TP:gm:i1_5:INDEL:het:26.74	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0		150089753
Common		GRCh37			6	chr6	150101478	149780342	0	FP	G	GA	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:.:i1_5:INDEL:het	CommonFP			no	yes	Likely an error in hifiasm in homopolymer due to region of high homozygosity													.:.:.:.:.:NOCALL:nocall	0/1:20.77:FP:.:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:251.73:FP:.:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:.:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:267.64:FP:.:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:.:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:48.97:FP:.:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:10:FP:.:i1_5:INDEL:het	6:150101478	149780342
Common		GRCh38			6	chr6	150101478	149780342	5091	FP	G	GA	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:.:i1_5:INDEL:het	CommonFP			no	yes	Likely an error in hifiasm in homopolymer due to region of high homozygosity													.:.:.:.:.:NOCALL:nocall	0/1:20.77:FP:.:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:239.73:FP:.:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:.:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:198.64:FP:.:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:.:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:48.98:FP:.:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:10:FP:.:i1_5:INDEL:het		150101478
CMH_DRAGEN_3.6.3	NA24385.hard-filtered.vcf.gz	GRCh37	small-variants	SNP	6	chr6	150106569	149785433	7729	FP_FN	C	T	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:ti:SNP:homalt	0/1:FP:am:49.49:ti:SNP:het	yes	no																															6:150106569	149785433
CMH_DRAGEN_3.6.3	NA24385.hard-filtered.vcf.gz	GRCh37	small-variants	INDEL	6	chr6	150114298	149793162	0	FP	CAA	C	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:216.25:FP:lm:d1_5:INDEL:het	unsure	unsure	In SINE. The query is well supported in general but  inconsistent among reads with same haplotags	no	yes	Likely an error in hifiasm in homopolymer due to region of high homozygosity																											6:150114298	149793162
Common		GRCh37			6	chr6	150114298	149793162	0	FP	CAA	C	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:lm:d1_5:INDEL:het	CommonFP			no	yes	Likely an error in hifiasm in homopolymer due to region of high homozygosity													./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:887.73:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:978.06:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:216.25:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	1/1:17:FP:lm:d1_5:INDEL:homalt	6:150114298	149793162
Common		GRCh37			6	chr6	150114298	149793162	0	FN	CA	C	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:am:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no	yes	Likely an error in hifiasm in homopolymer due to region of high homozygosity													1|1:FN:.:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:am:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:am:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:am:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:d1_5:INDEL:homalt:0	.:.:.:.:NOCALL:nocall:0	1|1:FN:am:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:lm:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	6:150114298	149793162
NCBI	HG002_grch38_dipcall.vcf.gz	GRCh38	small-variants	INDEL	6	chr6	150114298	149793162	0	FN	CA	C	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:am:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	usure	unsure	CSV ERROR here:  most likely query correct;  query: chr6    149793162       .       CAA     C,CA    30      .       .       GT:AD   1|2:0,1,1; 	no	yes	Likely an error in hifiasm in homopolymer due to region of high homozygosity																												150114298
BCM-HGSC_xAtlas	HG002.GRCh38.60x.1_merged.vcf.gz	GRCh38	small-variants	INDEL	6	chr6	150114298	149793162	0	FP	CAA	C	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	1/1:17:FP:lm:d1_5:INDEL:homalt 	Unsure	No	Illumina 60x, 10X phased and PacBio Sequel II suggest possible CAA->C,CA at chr6:149793162.	no	yes	Likely an error in hifiasm in homopolymer due to region of high homozygosity																												150114298
ITER	ITERteam_small-variation_GRCh38_ILMN-PB-ONT.vcf.gz	GRCh38	small-variants	INDEL	6	chr6	150114298	149793162	0	FN	CA	C	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:am:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	No	Yes	We called a variant with het genotype with a 2-bases deletion. Technologies support a deletion of more than 1 base at this site.	no	yes	Likely an error in hifiasm in homopolymer due to region of high homozygosity																												150114298
Common		GRCh38			6	chr6	150114298	149793162	0	FN	CA	C	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:am:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no	yes	Likely an error in hifiasm in homopolymer due to region of high homozygosity													1|1:FN:.:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:am:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:am:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:am:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:d1_5:INDEL:homalt:0	.:.:.:.:NOCALL:nocall:0	1|1:FN:am:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:lm:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0		150114298
Common		GRCh38			6	chr6	150114298	149793162	1	FP	CAA	C	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:lm:d1_5:INDEL:het	CommonFP			no	yes	Likely an error in hifiasm in homopolymer due to region of high homozygosity													./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:887.73:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:584.06:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:214.81:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	1/1:17:FP:lm:d1_5:INDEL:homalt		150114298
Common		GRCh37			6	chr6	150114299	149793163	0	FP	AA	A	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:am:d1_5:INDEL:het	CommonFP			no	yes	Likely an error in hifiasm in homopolymer due to region of high homozygosity													./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:887.73:FP:am:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:am:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:978.06:FP:am:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:0:TP:gm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:216.25:FP:am:d1_5:INDEL:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	6:150114299	149793163
Common		GRCh38			6	chr6	150114299	149793163	9456	FP	AA	A	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:am:d1_5:INDEL:het	CommonFP			no	yes	Likely an error in hifiasm in homopolymer due to region of high homozygosity													./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:887.73:FP:am:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:am:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:584.06:FP:am:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:0:TP:gm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:214.81:FP:am:d1_5:INDEL:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.		150114299
BCM-HGSC_xAtlas	HG002.hs37d5.60x.1_merged.vcf.gz	GRCh37	small-variants	SNP	6	chr6	150123755	149802619	18673865	FP_FN	G	T	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:tv:SNP:homalt	0/1:FP:am:26:tv:SNP:het 	Yes	No																															6:150123755	149802619
DNAnexus	hs37d5_HG002_WGS_union.vcf.gz	GRCh37	small-variants	INDEL	6	chr6	168877164	168476484	35327	FN	G	GTGTA	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	yes	no																															6:168877164	168476484
Common		GRCh37			6	chr6	168912491	168511811	11268	FP_FN	G	GTTT,GTTTT,GTTTTT	GT:BD:BK:QQ:BI:BVT:BLT	2|3:FN:am:.:i1_5:INDEL:hetalt	3/1:FP:am:100:i1_5:INDEL:hetalt	CommonFP_FN			unsure	unsure	all techs noisy in ins in long homopolymer													2|3:FN:am:.:i1_5:INDEL:hetalt	3/3:FP:am:1951.73:i1_5:INDEL:homalt	2|3:FN:lm:.:i1_5:INDEL:hetalt	1/1:FP:lm:1014.73:i1_5:INDEL:homalt	2|3:FN:am:.:i1_5:INDEL:hetalt	2/1:FP:am:30:i1_5:INDEL:hetalt	2|3:FN:am:.:i1_5:INDEL:hetalt	3/1:FP:am:895.1:i1_5:INDEL:hetalt	2|3:FN:am:.:i1_5:INDEL:hetalt	1/1:FP:lm:0:i1_5:INDEL:homalt	2|3:FN:am:.:i1_5:INDEL:hetalt	3/1:FP:am:252.38:i1_5:INDEL:hetalt	2|3:FN:lm:.:i1_5:INDEL:hetalt	0/1:FP:lm:8:i1_5:INDEL:het	6:168912491	168511811
NCBI	HG002_grch37_dipcall.vcf.gz	GRCh37	small-variants	INDEL	6	chr6	168923759	168523079	0	FP_FN	A	ATTCTTTTTTTTTT,ATTCTTTTTTTTTTT	GT:BD:BK:BI:QQ:BVT:BLT	2|1:FN:am:i6_15:.:INDEL:hetalt	1/1:FP:am:i6_15:30:INDEL:homalt	unsure	unsure	evidence for various Ts INS here; repeat region	unsure	unsure	benchmark may be correct but all techs are noisy in long ins in homopolymer																											6:168923759	168523079
Common		GRCh37			6	chr6	168923759	168523079	0	FP_FN	A	ATTCTTTTTTTTTT,ATTCTTTTTTTTTTT,ATTCTTTTTTTTTTTT,ATTTTTTTTTTTTT	GT:BD:BK:BI:BVT:BLT:QQ	2|1:FN:am:i6_15:INDEL:hetalt:.	1/1:FP:am:i6_15:INDEL:homalt:100	CommonFP_FN			unsure	unsure	benchmark may be correct but all techs are noisy in long ins in homopolymer													2|1:FN:am:i6_15:INDEL:hetalt:.	1/1:FP:am:i6_15:INDEL:homalt:1852.73	2|1:FN:.:i6_15:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:0	2|1:FN:am:i6_15:INDEL:hetalt:.	1/1:FP:am:i6_15:INDEL:homalt:30	2|1:FN:lm:i6_15:INDEL:hetalt:.	4/4:FP:lm:i6_15:INDEL:homalt:75.98	2|1:FN:lm:i6_15:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:0	2|1:FN:lm:i6_15:INDEL:hetalt:.	3/3:FP:lm:i6_15:INDEL:homalt:88.98	2|1:FN:lm:i6_15:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:0	6:168923759	168523079
Common		GRCh38			6	chr6	168923759	168523079	65997	FP_FN	A	ATTCTTTTTTTTTT,ATTCTTTTTTTTTTT,ATTCTTTTTTTTTTTT	GT:BD:BK:BI:QQ:BVT:BLT	2|1:FN:am:i6_15:.:INDEL:hetalt	1/1:FP:am:i6_15:100:INDEL:homalt	CommonFP_FN			unsure	unsure	benchmark may be correct but all techs are noisy in long ins in homopolymer													2|1:FN:am:i6_15:.:INDEL:hetalt	1/1:FP:am:i6_15:1852.73:INDEL:homalt	2|1:FN:.:i6_15:.:INDEL:hetalt	.:.:.:.:0:NOCALL:nocall	2|1:FN:am:i6_15:.:INDEL:hetalt	1/1:FP:am:i6_15:30:INDEL:homalt	2|1:FN:am:i6_15:.:INDEL:hetalt	1/1:FP:am:i6_15:175.89:INDEL:homalt	2|1:FN:lm:i6_15:.:INDEL:hetalt	.:.:.:.:0:NOCALL:nocall	2|1:FN:lm:i6_15:.:INDEL:hetalt	3/3:FP:lm:i6_15:88.98:INDEL:homalt	2|1:FN:lm:i6_15:.:INDEL:hetalt	.:.:.:.:0:NOCALL:nocall		168923759
ITER	ITERteam_small-variation_GRCh38_ILMN-PB-ONT.vcf.gz	GRCh38	small-variants	INDEL	6	chr6	168989756	168589076	1473	FN	CA	C	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	Unsure	Unsure	Only supported by some ILMN and 10x reads in truth and ILMN and PacBio in query.	unsure	unsure	benchmark appears likely correct since it's supported by PCR-free illumina, and average length of each haplotype on 10x and HiFi, but data is noisy so kept unsure																												168989756
NCBI	HG002_grch37_dipcall.vcf.gz	GRCh37	small-variants	SNP	6	chr6	168991229	168590549	41	FP_FN	G	T	GT:BD:BK:QQ:BI:BVT:BLT	0|1:FN:am:.:tv:SNP:het	1/1:FP:am:30:tv:SNP:homalt	yes	no 	evidence for HET 																														6:168991229	168590549
NCBI	HG002_grch38_dipcall.vcf.gz	GRCh38	small-variants	INDEL	6	chr6	168991270	168590590	636579	FP_FN	C	CT	GT:BD:BK:QQ:BI:BVT:BLT	0|1:FN:am:.:i1_5:INDEL:het	1/1:FP:am:30:i1_5:INDEL:homalt	yes	no	evidence for HET							skip																								168991270
ITER	ITERteam_small-variation_GRCh37_ILMN-PB-ONT.vcf.gz	GRCh37	small-variants	INDEL	6	chr6	169627264	169227169	16995	FP	GA	G	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:8.2:FP:lm:d1_5:INDEL:het	Yes	No																															6:169627264	169227169
CMH_DRAGEN_3.6.3	NA24385.hard-filtered.vcf.gz	GRCh37	small-variants	INDEL	6	chr6	169644259	169244164	-163960132	FN	GT	G	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	yes	no																															6:169644259	169244164
Common		GRCh37			7	chr7	5323663	5284032	7	FN	A	AC	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:lm:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no		at least the 4bp del in long C homopolymer looks like it should be 5bp del in illumina													0|1:TP:gm:i1_5:INDEL:het:60.73	0/1:TP:gm:i1_5:INDEL:het:60.73	0|1:FN:lm:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	7:5323663	5284032
Common		GRCh37			7	chr7	5323670	5284039	1	FP	CCCCCA	C	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:lm:d1_5:INDEL:het	CommonFP			no		at least the 4bp del in long C homopolymer looks like it should be 5bp del in illumina													./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:538.73:FP:lm:d1_5:INDEL:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:504.6:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:48.57:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:17:FP:lm:d1_5:INDEL:het	7:5323670	5284039
Common		GRCh37			7	chr7	5323671	5284040	6012	FN	CCCCA	C	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:lm:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no		at least the 4bp del in long C homopolymer looks like it should be 5bp del in illumina													1|0:FN:lm:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:lm:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:lm:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:lm:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:lm:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:lm:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	7:5323671	5284040
Common		GRCh37			7	chr7	5329683	5290052	0	FP_FN	A	ATTTT,ATTT,AT	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:lm:i1_5:INDEL:het:.	0/2:FP:lm:i1_5:INDEL:het:100	CommonFP_FN			no	yes	likely 3bp ins in long homopolymer since illumina supports it													1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:lm:i1_5:INDEL:het:.	0/2:FP:lm:i1_5:INDEL:het:321.73	1|0:FN:lm:i1_5:INDEL:het:.	0/2:FP:lm:i1_5:INDEL:het:30	1|0:FN:lm:i1_5:INDEL:het:.	3/3:FP:lm:i1_5:INDEL:homalt:5.2	1|0:FN:am:i1_5:INDEL:het:.	2/2:FP:lm:i1_5:INDEL:homalt:0	1|0:FN:lm:i1_5:INDEL:het:.	0/2:FP:lm:i1_5:INDEL:het:44.9	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	7:5329683	5290052
Common		GRCh38			7	chr7	5329683	5290052	39510346	FP_FN	A	ATTT,ATTTT	GT:BD:BK:QQ:BI:BVT:BLT	2|0:FN:lm:.:i1_5:INDEL:het	0/1:FP:lm:100:i1_5:INDEL:het	CommonFP_FN			no	yes	likely 3bp ins in long homopolymer since illumina supports it													2|0:FN:.:.:i1_5:INDEL:het	.:.:.:0:.:NOCALL:nocall	2|0:FN:lm:.:i1_5:INDEL:het	0/1:FP:lm:321.73:i1_5:INDEL:het	2|0:FN:lm:.:i1_5:INDEL:het	0/1:FP:lm:30:i1_5:INDEL:het	2|0:FN:lm:.:i1_5:INDEL:het	0/1:FP:lm:178.64:i1_5:INDEL:het	2|0:FN:am:.:i1_5:INDEL:het	1/1:FP:lm:0:i1_5:INDEL:homalt	2|0:FN:lm:.:i1_5:INDEL:het	0/1:FP:lm:44.89:i1_5:INDEL:het	2|0:FN:.:.:i1_5:INDEL:het	.:.:.:0:.:NOCALL:nocall		5329683
BCM-HGSC_xAtlas	HG002.hs37d5.60x.1_merged.vcf.gz	GRCh37	small-variants	INDEL	7	chr7	44839997	44800398	11248397	FP	C	CT	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	1/1:11:FP:lm:i1_5:INDEL:homalt 	Yes	No																															7:44839997	44800398
Common		GRCh37			7	chr7	56116488	56048795	0	FP_FN	C	CT,CTT	GT:BD:BK:BI:QQ:BVT:BLT	1|2:FN:am:i1_5:.:INDEL:hetalt	1/1:FP:am:i1_5:100:INDEL:homalt	CommonFP_FN			no	yes	likely hifiasm error in homopolymer due to noisy HiFi													1|2:FN:am:i1_5:.:INDEL:hetalt	1/1:FP:am:i1_5:339.73:INDEL:homalt	1|2:FN:am:i1_5:.:INDEL:hetalt	1/1:FP:am:i1_5:450.73:INDEL:homalt	1|2:FN:am:i1_5:.:INDEL:hetalt	1/1:FP:am:i1_5:30:INDEL:homalt	1|2:FN:am:i1_5:.:INDEL:hetalt	1/1:FP:am:i1_5:348.06:INDEL:homalt	1|2:FN:am:i1_5:.:INDEL:hetalt	1/1:FP:am:i1_5:0:INDEL:homalt	1|2:FN:am:i1_5:.:INDEL:hetalt	1/1:FP:am:i1_5:92.06:INDEL:homalt	1|2:FN:am:i1_5:.:INDEL:hetalt	1/1:FP:am:i1_5:9:INDEL:homalt	7:56116488	56048795
Common		GRCh38			7	chr7	56116488	56048795	18267093	FP_FN	C	CT,CTT	GT:BD:BK:BI:QQ:BVT:BLT	1|2:FN:am:i1_5:.:INDEL:hetalt	1/1:FP:am:i1_5:100:INDEL:homalt	CommonFP_FN			no	yes	likely hifiasm error in homopolymer due to noisy HiFi													1|2:FN:am:i1_5:.:INDEL:hetalt	1/1:FP:am:i1_5:339.73:INDEL:homalt	1|2:FN:am:i1_5:.:INDEL:hetalt	1/1:FP:am:i1_5:565.73:INDEL:homalt	1|2:FN:am:i1_5:.:INDEL:hetalt	1/1:FP:am:i1_5:30:INDEL:homalt	1|2:FN:am:i1_5:.:INDEL:hetalt	1/1:FP:am:i1_5:312.06:INDEL:homalt	1|2:FN:am:i1_5:.:INDEL:hetalt	1/1:FP:am:i1_5:0:INDEL:homalt	1|2:FN:am:i1_5:.:INDEL:hetalt	1/1:FP:am:i1_5:92.17:INDEL:homalt	1|2:FN:am:i1_5:.:INDEL:hetalt	1/1:FP:am:i1_5:8:INDEL:homalt		56116488
Common		GRCh37			7	chr7	73730218	74315888	0	FN	TA	T	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:lm:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no	yes	likely hifiasm error in adjacent homopolymers due to noisy HiFi													0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	7:73730218	74315888
Common		GRCh38			7	chr7	73730218	74315888	1	FN	TA	T	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:lm:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no	yes	likely hifiasm error in adjacent homopolymers due to noisy HiFi													0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0		73730218
NYGC	HG-002-2x250-b37.recalibrated.haplotypeCalls.vcf.gz	GRCh37	small-variants	SNP	7	chr7	73730219	74315889	0	FP	A	T	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:610.77:FP:lm:tv:SNP:het 	yes	no		no	yes	likely hifiasm error in adjacent homopolymers due to noisy HiFi																											7:73730219	74315889
Common		GRCh37			7	chr7	73730219	74315889	0	FP	A	T	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:lm:tv:SNP:het	CommonFP			no	yes	likely hifiasm error in adjacent homopolymers due to noisy HiFi													./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:610.77:FP:lm:tv:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:lm:tv:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:802.6:FP:lm:tv:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:lm:tv:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:50:FP:lm:tv:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:lm:tv:SNP:het	7:73730219	74315889
Common		GRCh38			7	chr7	73730219	74315889	8929	FP	A	T	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:lm:tv:SNP:het	CommonFP			no	yes	likely hifiasm error in adjacent homopolymers due to noisy HiFi													./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:699.77:FP:lm:tv:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:lm:tv:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:252.6:FP:lm:tv:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:lm:tv:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:50:FP:lm:tv:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:lm:tv:SNP:het		73730219
DNAnexus	hs37d5_HG002_WGS_union.vcf.gz	GRCh37	small-variants	INDEL	7	chr7	73739148	74324818	0	FP_FN	GA	G,GAA	GT:BD:BK:BI:QQ:BVT:BLT	2|1:FN:am:d1_5,i1_5:.:INDEL:hetalt	0/1:FP:am:d1_5:0:INDEL:het	unsure	no	This is variant is touching a homopolymer (A's) region. While one long-read data (PacBio) found a 2bp insertion, the raw reads of both PacBio and ONT suggest it a various length of deletion.	no	yes	likely hifiasm error in homopolymer due to noisy HiFi																											7:73739148	74324818
Common		GRCh37			7	chr7	73739148	74324818	0	FP_FN	GA	G,GAA	GT:BD:BK:BI:BVT:BLT:QQ	2|1:FN:am:d1_5,i1_5:INDEL:hetalt:.	0/1:FP:am:d1_5:INDEL:het:100	CommonFP_FN			no	yes	likely hifiasm error in homopolymer due to noisy HiFi													2|1:FN:.:d1_5,i1_5:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:0	2|1:FN:am:d1_5,i1_5:INDEL:hetalt:.	0/1:FP:am:d1_5:INDEL:het:186.73	2|1:FN:am:d1_5,i1_5:INDEL:hetalt:.	0/1:FP:am:d1_5:INDEL:het:30	2|1:FN:am:d1_5,i1_5:INDEL:hetalt:.	0/1:FP:am:d1_5:INDEL:het:56.6	2|1:FN:am:d1_5,i1_5:INDEL:hetalt:.	0/1:FP:am:d1_5:INDEL:het:0	2|1:FN:am:d1_5,i1_5:INDEL:hetalt:.	0/1:FP:am:d1_5:INDEL:het:35.75	2|1:FN:.:d1_5,i1_5:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:0	7:73739148	74324818
Common		GRCh38			7	chr7	73739148	74324818	7642	FP_FN	GA	G,GAA	GT:BD:BK:BI:QQ:BVT:BLT	2|1:FN:am:d1_5,i1_5:.:INDEL:hetalt	0/1:FP:am:d1_5:100:INDEL:het	CommonFP_FN			no	yes	likely hifiasm error in homopolymer due to noisy HiFi													2|1:FN:.:d1_5,i1_5:.:INDEL:hetalt	.:.:.:.:0:NOCALL:nocall	2|1:FN:am:d1_5,i1_5:.:INDEL:hetalt	0/1:FP:am:d1_5:225.77:INDEL:het	2|1:FN:am:d1_5,i1_5:.:INDEL:hetalt	0/1:FP:am:d1_5:30:INDEL:het	2|1:FN:am:d1_5,i1_5:.:INDEL:hetalt	0/1:FP:am:d1_5:134.6:INDEL:het	2|1:FN:am:d1_5,i1_5:.:INDEL:hetalt	0/1:FP:am:d1_5:0:INDEL:het	2|1:FN:am:d1_5,i1_5:.:INDEL:hetalt	0/1:FP:am:d1_5:33.94:INDEL:het	2|1:FN:.:d1_5,i1_5:.:INDEL:hetalt	.:.:.:.:0:NOCALL:nocall		73739148
DNAnexus	hs37d5_HG002_WGS_union.vcf.gz	GRCh37	small-variants	INDEL	7	chr7	73746790	74332460	16994	FP_FN	C	CTTTTT	GT:BD:BK:QQ:BI:BVT:BLT	0|1:FN:am:.:i1_5:INDEL:het	1/1:FP:am:0:i1_5:INDEL:homalt	unsure	no	This is right next to a homopolymer region (20 T's in the reference) The benchmark set (by PacBio) looks more correct than the query callset. However, ONT reads are suggesting mutlipe other complicated possibilities for this region. 																														7:73746790	74332460
Common		GRCh37			7	chr7	73763784	74349454	16	FN	ATG	A	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:lm:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no	yes	hifiasm appears to have extra 2bp del instead f SNV in long adjacent homopolymer and diTRs													0|1:FN:lm:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	7:73763784	74349454
Common		GRCh37			7	chr7	73763800	74349470	50072	FP	G	A	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:lm:ti:SNP:het	CommonFP			no	yes	hifiasm appears to have extra 2bp del instead f SNV in long adjacent homopolymer and diTRs													./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	1/1:717.12:FP:lm:ti:SNP:homalt	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:lm:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:53.57:FP:lm:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:32:FP:lm:ti:SNP:het	7:73763800	74349470
Common		GRCh37			7	chr7	73813872	74399542	0	FN	TG	T,TGG	GT:BD:BK:BI:BVT:BLT:QQ	2|1:TP:gm:d1_5,i1_5:INDEL:hetalt:100	0/1:TP:gm:d1_5:INDEL:het:100	CommonFN			unsure	unsure	all techs noisy in long G homopolymer													2|1:FN:.:d1_5,i1_5:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:0	2|1:FN:.:d1_5,i1_5:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:0	2|1:FN:.:d1_5,i1_5:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:0	2|1:FN:am:d1_5,i1_5:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:149.99	2|1:TP:gm:d1_5,i1_5:INDEL:hetalt:0	0/1:TP:gm:d1_5:INDEL:het:0	2|1:TP:gm:d1_5,i1_5:INDEL:hetalt:78.97	0/1:TP:gm:d1_5:INDEL:het:78.97	2|1:FN:lm:d1_5,i1_5:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:0	7:73813872	74399542
Common		GRCh38			7	chr7	73813872	74399542	3672	FN	TG	T,TGG	GT:BD:BK:QQ:BI:BVT:BLT	2|1:TP:gm:100:d1_5,i1_5:INDEL:hetalt	0/1:TP:gm:100:d1_5:INDEL:het	CommonFN			unsure	unsure	all techs noisy in long G homopolymer													2|1:FN:.:.:d1_5,i1_5:INDEL:hetalt	.:.:.:0:.:NOCALL:nocall	2|1:FN:.:.:d1_5,i1_5:INDEL:hetalt	.:.:.:0:.:NOCALL:nocall	2|1:FN:.:.:d1_5,i1_5:INDEL:hetalt	.:.:.:0:.:NOCALL:nocall	2|1:FN:.:.:d1_5,i1_5:INDEL:hetalt	.:.:.:0:.:NOCALL:nocall	2|1:TP:gm:0:d1_5,i1_5:INDEL:hetalt	0/1:TP:gm:0:d1_5:INDEL:het	2|1:TP:gm:78.39:d1_5,i1_5:INDEL:hetalt	0/1:TP:gm:78.39:d1_5:INDEL:het	2|1:FN:lm:.:d1_5,i1_5:INDEL:hetalt	.:.:.:0:.:NOCALL:nocall		73813872
NYGC	HG-002-2x250-b37.recalibrated.haplotypeCalls.vcf.gz	GRCh37	small-variants	INDEL	7	chr7	73817544	74403214	0	FP_FN	CA	C	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:255.73:d1_5:INDEL:het 	unsure	yes	There is evidence for reference allele on all the platforms. The hom-alt call is only see in Pacbio Hifi assembly.	no	yes	llikely hifiasm error missing haplotype in homopolymer in highly homozygous region																											7:73817544	74403214
Common		GRCh37			7	chr7	73817544	74403214	0	FP_FN	CA	C	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:am:d1_5:INDEL:homalt:.	0/1:FP:am:d1_5:INDEL:het:100	CommonFP_FN			no	yes	llikely hifiasm error missing haplotype in homopolymer in highly homozygous region													1|1:FN:am:d1_5:INDEL:homalt:.	0/1:FP:am:d1_5:INDEL:het:181.9	1|1:FN:am:d1_5:INDEL:homalt:.	0/1:FP:am:d1_5:INDEL:het:255.73	1|1:FN:am:d1_5:INDEL:homalt:.	0/1:FP:am:d1_5:INDEL:het:30	1|1:FN:am:d1_5:INDEL:homalt:.	0/1:FP:am:d1_5:INDEL:het:83.6	1|1:FN:am:d1_5:INDEL:homalt:.	0/1:FP:am:d1_5:INDEL:het:0	1|1:FN:am:d1_5:INDEL:homalt:.	0/1:FP:am:d1_5:INDEL:het:49.57	1|1:FN:.:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	7:73817544	74403214
PacBio_gatk4	gatk4hc_HG002_15kb_20kb_53X_SequelII.vcf.gz	GRCh38	small-variants	INDEL	7	chr7	73817544	74403214	0	FP_FN	CA	C	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:181.9:d1_5:INDEL:het	yes	no		no	yes	llikely hifiasm error missing haplotype in homopolymer in highly homozygous region				skip																								73817544
Common		GRCh38			7	chr7	73817544	74403214	335682	FP_FN	CA	C	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:100:d1_5:INDEL:het	CommonFP_FN			no	yes	llikely hifiasm error missing haplotype in homopolymer in highly homozygous region													1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:181.9:d1_5:INDEL:het	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:239.73:d1_5:INDEL:het	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:30:d1_5:INDEL:het	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:136.6:d1_5:INDEL:het	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:0:d1_5:INDEL:het	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:49.58:d1_5:INDEL:het	1|1:FN:.:.:d1_5:INDEL:homalt	.:.:.:0:.:NOCALL:nocall		73817544
Common		GRCh38			7	chr7	74153238	74738896	4768	FN	CAA	C	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:lm:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	Difficult to map and highly homozygous region, that has no haplotype partitioning for HiFi, but most variants except certain homopolymers appear to be supported by at least ONT and HiFi													1|1:TP:gm:d1_5:INDEL:homalt:367.74	1/1:TP:gm:d1_5:INDEL:homalt:367.74	1|1:FN:.:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:d1_5:INDEL:homalt:30	1/1:TP:gm:d1_5:INDEL:homalt:30	1|1:TP:gm:d1_5:INDEL:homalt:29.9	1/1:TP:gm:d1_5:INDEL:homalt:29.9	1|1:FN:.:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0		74153238
Common		GRCh38			7	chr7	74158003	74743664	30	FN	A	G	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:21.2:ti:SNP:homalt	1/1:TP:gm:21.2:ti:SNP:homalt	CommonFN			yes	no	Difficult to map and highly homozygous region, that has no haplotype partitioning for HiFi, but most variants except certain homopolymers appear to be supported by at least ONT and HiFi													1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:lm:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:TP:gm:30:ti:SNP:homalt	1/1:TP:gm:30:ti:SNP:homalt	1|1:TP:gm:34.4:ti:SNP:homalt	1/1:TP:gm:34.4:ti:SNP:homalt	1|1:FN:lm:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:lm:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall		74158003
BCM-HGSC_xAtlas	HG002.GRCh38.60x.1_merged.vcf.gz	GRCh38	small-variants	SNP	7	chr7	74158033	74743694	189	FP_FN	G	T	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:tv:SNP:homalt	0/1:FP:am:26:tv:SNP:het 	Yes	No		yes	no	Difficult to map and highly homozygous region, that has no haplotype partitioning for HiFi, but most variants except certain homopolymers appear to be supported by at least ONT and HiFi				skip																								74158033
Common		GRCh38			7	chr7	74158222	74743883	2225	FN	C	CA	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:100:i1_5:INDEL:homalt	1/1:TP:gm:100:i1_5:INDEL:homalt	CommonFN			yes	no	Difficult to map and highly homozygous region, that has no haplotype partitioning for HiFi, but most variants except certain homopolymers appear to be supported by at least ONT and HiFi													1|1:FN:.:.:i1_5:INDEL:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:i1_5:INDEL:homalt	.:.:.:0:.:NOCALL:nocall	1|1:TP:gm:30:i1_5:INDEL:homalt	1/1:TP:gm:30:i1_5:INDEL:homalt	1|1:FN:.:.:i1_5:INDEL:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:i1_5:INDEL:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:i1_5:INDEL:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:i1_5:INDEL:homalt	.:.:.:0:.:NOCALL:nocall		74158222
PacBio_gatk4	gatk4hc_HG002_15kb_20kb_53X_SequelII.vcf.gz	GRCh38	small-variants	SNP	7	chr7	74160447	74746108	190	FN	T	A	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	yes	no		yes	no	Difficult to map and highly homozygous region, that has no haplotype partitioning for HiFi, but most variants except certain homopolymers appear to be supported by at least ONT and HiFi				skip																								74160447
Roche	RN_HG002_Illumina_PacBio_Oxford_GRCh37.vcf.gz	GRCh37	small-variants	SNP	7	chr7	74160637	74746298	439	FP	T	C	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:12.2484:FP:.:ti:SNP:het 	yes	no																															7:74160637	74746298
Common		GRCh38			7	chr7	74161075	74746737	3540	FN	G	C	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:33.0111:tv:SNP:homalt	1/1:TP:gm:33.0111:tv:SNP:homalt	CommonFN			yes	no	Difficult to map and highly homozygous region, that has no haplotype partitioning for HiFi, but most variants except certain homopolymers appear to be supported by at least ONT and HiFi													1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:TP:gm:30:tv:SNP:homalt	1/1:TP:gm:30:tv:SNP:homalt	1|1:TP:gm:29.6:tv:SNP:homalt	1/1:TP:gm:29.6:tv:SNP:homalt	1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall		74161075
Common		GRCh37			7	chr7	74164614	74750277	0	FN	C	CA	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	CommonFN			unsure	unsure	little coverage except HiFi and ONT, and HiFi reads are a bit noisy and not haplotype-partitioned in highly homozygous region													1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:i1_5:INDEL:homalt:30	1/1:TP:gm:i1_5:INDEL:homalt:30	1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	7:74164614	74750277
Common		GRCh38			7	chr7	74164614	74750277	781	FN	C	CA	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	CommonFN			unsure	unsure	little coverage except HiFi and ONT, and HiFi reads are a bit noisy and not haplotype-partitioned in highly homozygous region													1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:i1_5:INDEL:homalt:30	1/1:TP:gm:i1_5:INDEL:homalt:30	1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0		74164614
Common		GRCh38			7	chr7	74165390	74751058	1344	FN	G	C	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:100:tv:SNP:homalt	1/1:TP:gm:100:tv:SNP:homalt	CommonFN			yes	no	Difficult to map and highly homozygous region, that has no haplotype partitioning for HiFi, but most variants except certain homopolymers appear to be supported by at least ONT and HiFi													1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:TP:gm:30:tv:SNP:homalt	1/1:TP:gm:30:tv:SNP:homalt	1|1:TP:gm:30:tv:SNP:homalt	1/1:TP:gm:30:tv:SNP:homalt	1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall		74165390
NCBI	HG002_grch37_dipcall.vcf.gz	GRCh37	small-variants	SNP	7	chr7	74166734	74752402	1517	FP	G	T	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	1/1:30:FP:.:tv:SNP:homalt	yes	no	segdup region; only 15% PB evidence for query																														7:74166734	74752402
Common		GRCh38			7	chr7	74168251	74753919	1154	FN	A	G	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:100:ti:SNP:homalt	1/1:TP:gm:100:ti:SNP:homalt	CommonFN			yes	no	Difficult to map and highly homozygous region, that has no haplotype partitioning for HiFi, but most variants except certain homopolymers appear to be supported by at least ONT and HiFi													1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:TP:gm:30:ti:SNP:homalt	1/1:TP:gm:30:ti:SNP:homalt	1|1:TP:gm:30.8:ti:SNP:homalt	1/1:TP:gm:30.8:ti:SNP:homalt	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall		74168251
Common		GRCh38			7	chr7	74169405	74755073	1390	FN	A	G	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:100:ti:SNP:homalt	1/1:TP:gm:100:ti:SNP:homalt	CommonFN			yes	no	Difficult to map and highly homozygous region, that has no haplotype partitioning for HiFi, but most variants except certain homopolymers appear to be supported by at least ONT and HiFi													1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:TP:gm:30:ti:SNP:homalt	1/1:TP:gm:30:ti:SNP:homalt	1|1:TP:gm:34.3:ti:SNP:homalt	1/1:TP:gm:34.3:ti:SNP:homalt	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall		74169405
Common		GRCh38			7	chr7	74170795	74756463	450	FN	A	G	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:100:ti:SNP:homalt	1/1:TP:gm:100:ti:SNP:homalt	CommonFN			yes	no	Difficult to map and highly homozygous region, that has no haplotype partitioning for HiFi, but most variants except certain homopolymers appear to be supported by at least ONT and HiFi													1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:TP:gm:30:ti:SNP:homalt	1/1:TP:gm:30:ti:SNP:homalt	1|1:TP:gm:25.8:ti:SNP:homalt	1/1:TP:gm:25.8:ti:SNP:homalt	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall		74170795
Common		GRCh38			7	chr7	74171245	74756913	23	FN	A	AC	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:100:i1_5:INDEL:homalt	1/1:TP:gm:100:i1_5:INDEL:homalt	CommonFN			yes	no	Difficult to map and highly homozygous region, that has no haplotype partitioning for HiFi, but most variants except certain homopolymers appear to be supported by at least ONT and HiFi													1|1:FN:.:.:i1_5:INDEL:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:i1_5:INDEL:homalt	.:.:.:0:.:NOCALL:nocall	1|1:TP:gm:30:i1_5:INDEL:homalt	1/1:TP:gm:30:i1_5:INDEL:homalt	1|1:TP:gm:14.5:i1_5:INDEL:homalt	1/1:TP:gm:14.5:i1_5:INDEL:homalt	1|1:FN:.:.:i1_5:INDEL:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:i1_5:INDEL:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:i1_5:INDEL:homalt	.:.:.:0:.:NOCALL:nocall		74171245
Common		GRCh38			7	chr7	74171269	74756936	308	FN	T	C	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:36.989:ti:SNP:homalt	1/1:TP:gm:36.989:ti:SNP:homalt	CommonFN			yes	no	Difficult to map and highly homozygous region, that has no haplotype partitioning for HiFi, but most variants except certain homopolymers appear to be supported by at least ONT and HiFi													1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:TP:gm:30:ti:SNP:homalt	1/1:TP:gm:30:ti:SNP:homalt	1|1:TP:gm:19.6:ti:SNP:homalt	1/1:TP:gm:19.6:ti:SNP:homalt	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall		74171269
Common		GRCh38			7	chr7	74171577	74757244	498	FN	C	G	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:100:tv:SNP:homalt	1/1:TP:gm:100:tv:SNP:homalt	CommonFN			yes	no	Difficult to map and highly homozygous region, that has no haplotype partitioning for HiFi, but most variants except certain homopolymers appear to be supported by at least ONT and HiFi													1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:TP:gm:30:tv:SNP:homalt	1/1:TP:gm:30:tv:SNP:homalt	1|1:TP:gm:33.6:tv:SNP:homalt	1/1:TP:gm:33.6:tv:SNP:homalt	1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall		74171577
Common		GRCh38			7	chr7	74172075	74757742	2083	FN	C	T	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:100:ti:SNP:homalt	1/1:TP:gm:100:ti:SNP:homalt	CommonFN			yes	no	Difficult to map and highly homozygous region, that has no haplotype partitioning for HiFi, but most variants except certain homopolymers appear to be supported by at least ONT and HiFi													1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:TP:gm:30:ti:SNP:homalt	1/1:TP:gm:30:ti:SNP:homalt	1|1:TP:gm:32.7:ti:SNP:homalt	1/1:TP:gm:32.7:ti:SNP:homalt	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall		74172075
DNAnexus	hs37d5_HG002_WGS_union.vcf.gz	GRCh37	small-variants	SNP	7	chr7	74174155	74759825	16891	FP_FN	T	G	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:tv:SNP:homalt	0/1:FP:am:0:tv:SNP:het	unsure	no	PacBio, Illumina and 10x Genomics reads all suggest it is homalt. Though, ONT data is showing there are 50% of the reads as "N", while 34% as "G".	yes	no	Difficult to map and highly homozygous region, that has no haplotype partitioning for HiFi, but most variants except certain homopolymers appear to be supported by at least ONT and HiFi																											7:74174155	74759825
Common		GRCh37			7	chr7	74191062	74776716	0	FN	G	GTCCCCTCCCCTCTCCTCCTGTCCCCTCCCT	GT:BD:BK:BI:BVT:BLT:QQ	1|1:TP:gm:i16_plus:INDEL:homalt:11.2079	1/1:TP:gm:i16_plus:INDEL:homalt:11.2079	CommonFN			yes	no	Difficult to map and highly homozygous region, that has no haplotype partitioning for HiFi, but most variants except certain homopolymers appear to be supported by at least ONT and HiFi													1|1:TP:gm:i16_plus:INDEL:homalt:592.73	1/1:TP:gm:i16_plus:INDEL:homalt:592.73	1|1:TP:gm:i16_plus:INDEL:homalt:53.7	1/1:TP:gm:i16_plus:INDEL:homalt:53.7	1|1:FN:.:i16_plus:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:i16_plus:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:i16_plus:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:i16_plus:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:lm:i16_plus:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	7:74191062	74776716
Common		GRCh38			7	chr7	74191062	74776716	3665	FN	G	GTCCCCTCCCCTCTCCTCCTGTCCCCTCCCT	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:.:i16_plus:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	Difficult to map and highly homozygous region, that has no haplotype partitioning for HiFi, but most variants except certain homopolymers appear to be supported by at least ONT and HiFi													1|1:TP:gm:i16_plus:INDEL:homalt:502.73	1/1:TP:gm:i16_plus:INDEL:homalt:502.73	1|1:FN:.:i16_plus:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:i16_plus:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:i16_plus:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:i16_plus:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:i16_plus:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:lm:i16_plus:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0		74191062
Common		GRCh38			7	chr7	74194727	74780381	2101	FN	C	T	GT:BD:BK:QQ:BI:BVT:BLT	0|1:TP:gm:100:ti:SNP:het	0/1:TP:gm:100:ti:SNP:het	CommonFN			yes	no	Difficult to map and highly homozygous region, that has no haplotype partitioning for HiFi, but most variants except certain homopolymers appear to be supported by at least ONT and HiFi													0|1:TP:gm:413.77:ti:SNP:het	0/1:TP:gm:413.77:ti:SNP:het	0|1:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:TP:gm:164.66:ti:SNP:het	0/1:TP:gm:164.66:ti:SNP:het	0|1:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall		74194727
BCM-HGSC_xAtlas	HG002.GRCh38.60x.1_merged.vcf.gz	GRCh38	small-variants	SNP	7	chr7	74196825	74782482	3691	FP_FN	A	G	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:ti:SNP:homalt	0/1:FP:am:19:ti:SNP:het 	Yes	No		yes	no	Difficult to map and highly homozygous region, that has no haplotype partitioning for HiFi, but most variants except certain homopolymers appear to be supported by at least ONT and HiFi				skip																								74196825
CMH_DRAGEN_3.6.3	NA24385.hard-filtered.vcf.gz	GRCh38	small-variants	SNP	7	chr7	74200517	74786173	16029	FP_FN	T	A	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:tv:SNP:homalt	0/1:FP:am:34.98:tv:SNP:het	yes	no		yes	no	Difficult to map and highly homozygous region, that has no haplotype partitioning for HiFi, but most variants except certain homopolymers appear to be supported by at least ONT and HiFi				skip																								74200517
CMH_DRAGEN_3.6.3	NA24385.hard-filtered.vcf.gz	GRCh38	small-variants	SNP	7	chr7	74216543	74802202	2374	FN	G	T	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	yes	no	Barely covered by short reads	yes	no	Difficult to map and highly homozygous region, that has no haplotype partitioning for HiFi, but most variants except certain homopolymers appear to be supported by at least ONT and HiFi				skip																								74216543
NCBI	HG002_grch37_dipcall.vcf.gz	GRCh37	small-variants	INDEL	7	chr7	74218917	74804576	653	FP	G	GT	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	1/1:30:FP:.:i1_5:INDEL:homalt	yes	no	segdup region; weak evidence for INS here																														7:74218917	74804576
CMH_DRAGEN_3.6.3	NA24385.hard-filtered.vcf.gz	GRCh38	small-variants	SNP	7	chr7	74219570	74805229	0	FN	T	C	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	yes	no	Barely covered by short reads	yes	no	Difficult to map and highly homozygous region, that has no haplotype partitioning for HiFi, but most variants except certain homopolymers appear to be supported by at least ONT and HiFi				skip																								74219570
Common		GRCh38			7	chr7	74219570	74805229	40	FN	T	C	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:100:ti:SNP:homalt	1/1:TP:gm:100:ti:SNP:homalt	CommonFN			yes	no	Difficult to map and highly homozygous region, that has no haplotype partitioning for HiFi, but most variants except certain homopolymers appear to be supported by at least ONT and HiFi													1|1:TP:gm:23.76:ti:SNP:homalt	1/1:TP:gm:23.76:ti:SNP:homalt	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:lm:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:TP:gm:15.2:ti:SNP:homalt	1/1:TP:gm:15.2:ti:SNP:homalt	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall		74219570
NCBI	HG002_grch38_dipcall.vcf.gz	GRCh38	small-variants	SNP	7	chr7	74219610	74805269	2015	FP	C	T	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	1/1:30:FP:.:ti:SNP:homalt	yes	no	segdup region	yes	no	Difficult to map and highly homozygous region, that has no haplotype partitioning for HiFi, but most variants except certain homopolymers appear to be supported by at least ONT and HiFi				skip																								74219610
Common		GRCh37			7	chr7	74221622	74807284	569	FN	AT	A	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:.:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	CommonFN			unsure	unsure	little coverage except HiFi and ONT, and HiFi reads are a bit noisy and not haplotype-partitioned in highly homozygous region													1|1:FN:.:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:lm:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:30	1|1:FN:.:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	7:74221622	74807284
Common		GRCh37			7	chr7	74222191	74807853	327	FN	T	A	GT:BD:BK:BI:BVT:BLT:QQ	1|1:TP:gm:tv:SNP:homalt:100	1/1:TP:gm:tv:SNP:homalt:100	CommonFN			yes	no	Difficult to map and highly homozygous region, that has no haplotype partitioning for HiFi, but most variants except certain homopolymers appear to be supported by at least ONT and HiFi													1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:tv:SNP:homalt:30	1/1:TP:gm:tv:SNP:homalt:30	1|1:TP:gm:tv:SNP:homalt:33.1	1/1:TP:gm:tv:SNP:homalt:33.1	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	7:74222191	74807853
Common		GRCh37			7	chr7	74222518	74808180	0	FN	T	G	GT:BD:BK:BI:BVT:BLT:QQ	1|1:TP:gm:tv:SNP:homalt:100	1/1:TP:gm:tv:SNP:homalt:100	CommonFN			yes	no	Difficult to map and highly homozygous region, that has no haplotype partitioning for HiFi, but most variants except certain homopolymers appear to be supported by at least ONT and HiFi													1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:tv:SNP:homalt:30	1/1:TP:gm:tv:SNP:homalt:30	1|1:TP:gm:tv:SNP:homalt:32.6	1/1:TP:gm:tv:SNP:homalt:32.6	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	7:74222518	74808180
Common		GRCh38			7	chr7	74222518	74808180	521	FN	T	G	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:100:tv:SNP:homalt	1/1:TP:gm:100:tv:SNP:homalt	CommonFN			yes	no	Difficult to map and highly homozygous region, that has no haplotype partitioning for HiFi, but most variants except certain homopolymers appear to be supported by at least ONT and HiFi													1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:TP:gm:30:tv:SNP:homalt	1/1:TP:gm:30:tv:SNP:homalt	1|1:TP:gm:13.2:tv:SNP:homalt	1/1:TP:gm:13.2:tv:SNP:homalt	1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall		74222518
Common		GRCh37			7	chr7	74223039	74808701	0	FN	T	C	GT:BD:BK:BI:BVT:BLT:QQ	1|1:TP:gm:ti:SNP:homalt:100	1/1:TP:gm:ti:SNP:homalt:100	CommonFN			yes	no	Difficult to map and highly homozygous region, that has no haplotype partitioning for HiFi, but most variants except certain homopolymers appear to be supported by at least ONT and HiFi													1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:ti:SNP:homalt:30	1/1:TP:gm:ti:SNP:homalt:30	1|1:TP:gm:ti:SNP:homalt:31.6	1/1:TP:gm:ti:SNP:homalt:31.6	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	7:74223039	74808701
Common		GRCh38			7	chr7	74223039	74808701	163	FN	T	C	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:100:ti:SNP:homalt	1/1:TP:gm:100:ti:SNP:homalt	CommonFN			yes	no	Difficult to map and highly homozygous region, that has no haplotype partitioning for HiFi, but most variants except certain homopolymers appear to be supported by at least ONT and HiFi													1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:TP:gm:30:ti:SNP:homalt	1/1:TP:gm:30:ti:SNP:homalt	1|1:TP:gm:14.6:ti:SNP:homalt	1/1:TP:gm:14.6:ti:SNP:homalt	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall		74223039
Common		GRCh37			7	chr7	74223201	74808864	0	FN	A	G	GT:BD:BK:BI:BVT:BLT:QQ	1|1:TP:gm:ti:SNP:homalt:100	1/1:TP:gm:ti:SNP:homalt:100	CommonFN			yes	no	Difficult to map and highly homozygous region, that has no haplotype partitioning for HiFi, but most variants except certain homopolymers appear to be supported by at least ONT and HiFi													1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:ti:SNP:homalt:30	1/1:TP:gm:ti:SNP:homalt:30	1|1:TP:gm:ti:SNP:homalt:25.9	1/1:TP:gm:ti:SNP:homalt:25.9	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	7:74223201	74808864
Roche	RN_HG002_Illumina_PacBio_Oxford.vcf.gz	GRCh38	small-variants	SNP	7	chr7	74223201	74808864	541	FP_FN	A	G	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:ti:SNP:homalt	0/1:FP:am:100:ti:SNP:het 	yes	no		yes	no	Difficult to map and highly homozygous region, that has no haplotype partitioning for HiFi, but most variants except certain homopolymers appear to be supported by at least ONT and HiFi				skip																								74223201
Common		GRCh37			7	chr7	74223742	74809405	326769	FN	T	C	GT:BD:BK:BI:BVT:BLT:QQ	1|1:TP:gm:ti:SNP:homalt:33.0106	1/1:TP:gm:ti:SNP:homalt:33.0106	CommonFN			yes	no	Region in GTF2iRD2 that appears different in GRCh37 and 38, so that HG002 has a homozygous 195bp del relative to GRCh37 that causes low cov except ONT. Difficult to map and highly homozygous region, that has no haplotype partitioning for HiFi, but most variants except certain homopolymers appear to be supported by at least ONT and HiFi													1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:ti:SNP:homalt:30	1/1:TP:gm:ti:SNP:homalt:30	1|1:TP:gm:ti:SNP:homalt:25.5	1/1:TP:gm:ti:SNP:homalt:25.5	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	7:74223742	74809405
Common		GRCh37			7	chr7	74224315	75136174	-102	FN	T	TTTA	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	Region in GTF2iRD2 that appears different in GRCh37 and 38, so that HG002 has a homozygous 195bp del relative to GRCh37 that causes low cov except ONT. Difficult to map and highly homozygous region, that has no haplotype partitioning for HiFi, but most variants except certain homopolymers appear to be supported by at least ONT and HiFi													1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:i1_5:INDEL:homalt:30	1/1:TP:gm:i1_5:INDEL:homalt:30	1|1:TP:gm:i1_5:INDEL:homalt:20.5	1/1:TP:gm:i1_5:INDEL:homalt:20.5	1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	7:74224315	75136174
Common		GRCh37			7	chr7	74224414	75136072	-719	FN	G	A	GT:BD:BK:BI:BVT:BLT:QQ	1|1:TP:gm:ti:SNP:homalt:100	1/1:TP:gm:ti:SNP:homalt:100	CommonFN			yes	no	Region in GTF2iRD2 that appears different in GRCh37 and 38, so that HG002 has a homozygous 195bp del relative to GRCh37 that causes low cov except ONT. Difficult to map and highly homozygous region, that has no haplotype partitioning for HiFi, but most variants except certain homopolymers appear to be supported by at least ONT and HiFi													1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:ti:SNP:homalt:30	1/1:TP:gm:ti:SNP:homalt:30	1|1:TP:gm:ti:SNP:homalt:31	1/1:TP:gm:ti:SNP:homalt:31	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	7:74224414	75136072
Common		GRCh37			7	chr7	74225133	75135353	-208	FN	A	G	GT:BD:BK:BI:BVT:BLT:QQ	1|1:TP:gm:ti:SNP:homalt:100	1/1:TP:gm:ti:SNP:homalt:100	CommonFN			yes	no	Region in GTF2iRD2 that appears different in GRCh37 and 38, so that HG002 has a homozygous 195bp del relative to GRCh37 that causes low cov except ONT. Difficult to map and highly homozygous region, that has no haplotype partitioning for HiFi, but most variants except certain homopolymers appear to be supported by at least ONT and HiFi													1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:ti:SNP:homalt:30	1/1:TP:gm:ti:SNP:homalt:30	1|1:TP:gm:ti:SNP:homalt:32.6	1/1:TP:gm:ti:SNP:homalt:32.6	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	7:74225133	75135353
Common		GRCh37			7	chr7	74225341	75135145	-236	FN	GA	G	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:.:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	Region in GTF2iRD2 that appears different in GRCh37 and 38, so that HG002 has a homozygous 195bp del relative to GRCh37 that causes low cov except ONT. Difficult to map and highly homozygous region, that has no haplotype partitioning for HiFi, but most variants except certain homopolymers appear to be supported by at least ONT and HiFi													1|1:FN:.:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:d1_5:INDEL:homalt:30	1/1:TP:gm:d1_5:INDEL:homalt:30	1|1:FN:.:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	7:74225341	75135145
Common		GRCh37			7	chr7	74225578	75134909	-57	FN	A	G	GT:BD:BK:BI:BVT:BLT:QQ	1|1:TP:gm:ti:SNP:homalt:33.0111	1/1:TP:gm:ti:SNP:homalt:33.0111	CommonFN			yes	no	Region in GTF2iRD2 that appears different in GRCh37 and 38, so that HG002 has a homozygous 195bp del relative to GRCh37 that causes low cov except ONT. Difficult to map and highly homozygous region, that has no haplotype partitioning for HiFi, but most variants except certain homopolymers appear to be supported by at least ONT and HiFi													1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:ti:SNP:homalt:27.5	1/1:TP:gm:ti:SNP:homalt:27.5	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	7:74225578	75134909
Common		GRCh37			7	chr7	74225635	75134852	-7	FN	G	A	GT:BD:BK:BI:BVT:BLT:QQ	1|1:TP:gm:ti:SNP:homalt:100	1/1:TP:gm:ti:SNP:homalt:100	CommonFN			yes	no	Region in GTF2iRD2 that appears different in GRCh37 and 38, so that HG002 has a homozygous 195bp del relative to GRCh37 that causes low cov except ONT. Difficult to map and highly homozygous region, that has no haplotype partitioning for HiFi, but most variants except certain homopolymers appear to be supported by at least ONT and HiFi													1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:lm:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:ti:SNP:homalt:28.7	1/1:TP:gm:ti:SNP:homalt:28.7	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	7:74225635	75134852
Common		GRCh37			7	chr7	74225642	75134845	-468	FN	T	C	GT:BD:BK:BI:BVT:BLT:QQ	1|1:TP:gm:ti:SNP:homalt:100	1/1:TP:gm:ti:SNP:homalt:100	CommonFN			yes	no	Region in GTF2iRD2 that appears different in GRCh37 and 38, so that HG002 has a homozygous 195bp del relative to GRCh37 that causes low cov except ONT. Difficult to map and highly homozygous region, that has no haplotype partitioning for HiFi, but most variants except certain homopolymers appear to be supported by at least ONT and HiFi													1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:ti:SNP:homalt:30	1/1:TP:gm:ti:SNP:homalt:30	1|1:TP:gm:ti:SNP:homalt:33	1/1:TP:gm:ti:SNP:homalt:33	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	7:74225642	75134845
Common		GRCh37			7	chr7	74226110	75134377	-357	FN	C	T	GT:BD:BK:BI:BVT:BLT:QQ	1|1:TP:gm:ti:SNP:homalt:100	1/1:TP:gm:ti:SNP:homalt:100	CommonFN			yes	no	Region in GTF2iRD2 that appears different in GRCh37 and 38, so that HG002 has a homozygous 195bp del relative to GRCh37 that causes low cov except ONT. Difficult to map and highly homozygous region, that has no haplotype partitioning for HiFi, but most variants except certain homopolymers appear to be supported by at least ONT and HiFi													1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:ti:SNP:homalt:33.5	1/1:TP:gm:ti:SNP:homalt:33.5	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	7:74226110	75134377
Common		GRCh37			7	chr7	74226465	75134020	-346	FN	T	G	GT:BD:BK:BI:BVT:BLT:QQ	1|1:TP:gm:tv:SNP:homalt:100	1/1:TP:gm:tv:SNP:homalt:100	CommonFN			yes	no	Region in GTF2iRD2 that appears different in GRCh37 and 38, so that HG002 has a homozygous 195bp del relative to GRCh37 that causes low cov except ONT. Difficult to map and highly homozygous region, that has no haplotype partitioning for HiFi, but most variants except certain homopolymers appear to be supported by at least ONT and HiFi													1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:tv:SNP:homalt:30	1/1:TP:gm:tv:SNP:homalt:30	1|1:TP:gm:tv:SNP:homalt:30.1	1/1:TP:gm:tv:SNP:homalt:30.1	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	7:74226465	75134020
Common		GRCh37			7	chr7	74226811	75133674	-283	FN	G	C	GT:BD:BK:BI:BVT:BLT:QQ	1|1:TP:gm:tv:SNP:homalt:100	1/1:TP:gm:tv:SNP:homalt:100	CommonFN			yes	no	Region in GTF2iRD2 that appears different in GRCh37 and 38, so that HG002 has a homozygous 195bp del relative to GRCh37 that causes low cov except ONT. Difficult to map and highly homozygous region, that has no haplotype partitioning for HiFi, but most variants except certain homopolymers appear to be supported by at least ONT and HiFi													1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:tv:SNP:homalt:28.8	1/1:TP:gm:tv:SNP:homalt:28.8	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	7:74226811	75133674
Common		GRCh37			7	chr7	74227093	75133391	-67	FN	G	A	GT:BD:BK:BI:BVT:BLT:QQ	1|1:TP:gm:ti:SNP:homalt:100	1/1:TP:gm:ti:SNP:homalt:100	CommonFN			yes	no	Region in GTF2iRD2 that appears different in GRCh37 and 38, so that HG002 has a homozygous 195bp del relative to GRCh37 that causes low cov except ONT. Difficult to map and highly homozygous region, that has no haplotype partitioning for HiFi, but most variants except certain homopolymers appear to be supported by at least ONT and HiFi													1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:ti:SNP:homalt:30	1/1:TP:gm:ti:SNP:homalt:30	1|1:TP:gm:ti:SNP:homalt:37.1	1/1:TP:gm:ti:SNP:homalt:37.1	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	7:74227093	75133391
Common		GRCh37			7	chr7	74227160	75133324	-491	FN	A	T	GT:BD:BK:BI:BVT:BLT:QQ	1|1:TP:gm:tv:SNP:homalt:100	1/1:TP:gm:tv:SNP:homalt:100	CommonFN			yes	no	Region in GTF2iRD2 that appears different in GRCh37 and 38, so that HG002 has a homozygous 195bp del relative to GRCh37 that causes low cov except ONT. Difficult to map and highly homozygous region, that has no haplotype partitioning for HiFi, but most variants except certain homopolymers appear to be supported by at least ONT and HiFi													1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:tv:SNP:homalt:30	1/1:TP:gm:tv:SNP:homalt:30	1|1:TP:gm:tv:SNP:homalt:23.3	1/1:TP:gm:tv:SNP:homalt:23.3	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	7:74227160	75133324
Common		GRCh37			7	chr7	74227651	75132833	-23	FN	C	T	GT:BD:BK:BI:BVT:BLT:QQ	1|1:TP:gm:ti:SNP:homalt:100	1/1:TP:gm:ti:SNP:homalt:100	CommonFN			yes	no	Region in GTF2iRD2 that appears different in GRCh37 and 38, so that HG002 has a homozygous 195bp del relative to GRCh37 that causes low cov except ONT. Difficult to map and highly homozygous region, that has no haplotype partitioning for HiFi, but most variants except certain homopolymers appear to be supported by at least ONT and HiFi													1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:ti:SNP:homalt:31.3	1/1:TP:gm:ti:SNP:homalt:31.3	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	7:74227651	75132833
Common		GRCh37			7	chr7	74227674	75132810	-303	FN	G	A	GT:BD:BK:BI:BVT:BLT:QQ	1|1:TP:gm:ti:SNP:homalt:100	1/1:TP:gm:ti:SNP:homalt:100	CommonFN			yes	no	Region in GTF2iRD2 that appears different in GRCh37 and 38, so that HG002 has a homozygous 195bp del relative to GRCh37 that causes low cov except ONT. Difficult to map and highly homozygous region, that has no haplotype partitioning for HiFi, but most variants except certain homopolymers appear to be supported by at least ONT and HiFi													1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:ti:SNP:homalt:31	1/1:TP:gm:ti:SNP:homalt:31	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	7:74227674	75132810
Common		GRCh37			7	chr7	74227976	75132507	-915	FN	C	G	GT:BD:BK:BI:BVT:BLT:QQ	1|1:TP:gm:tv:SNP:homalt:9.309	1/1:TP:gm:tv:SNP:homalt:9.309	CommonFN			yes	no	Region in GTF2iRD2 that appears different in GRCh37 and 38, so that HG002 has a homozygous 195bp del relative to GRCh37 that causes low cov except ONT. Difficult to map and highly homozygous region, that has no haplotype partitioning for HiFi, but most variants except certain homopolymers appear to be supported by at least ONT and HiFi													1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:tv:SNP:homalt:30	1/1:TP:gm:tv:SNP:homalt:30	1|1:TP:gm:tv:SNP:homalt:37.3	1/1:TP:gm:tv:SNP:homalt:37.3	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	7:74227976	75132507
PacBio_gatk4	gatk4hc_HG002_15kb_20kb_52X_SequelII.vcf.gz	GRCh37	small-variants	SNP	7	chr7	74228889	75131592	0	FN	T	C	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	yes	no		yes	no	Region in GTF2iRD2 that appears different in GRCh37 and 38, so that HG002 has a homozygous 195bp del relative to GRCh37 that causes low cov except ONT. Difficult to map and highly homozygous region, that has no haplotype partitioning for HiFi, but most variants except certain homopolymers appear to be supported by at least ONT and HiFi																											7:74228889	75131592
Common		GRCh37			7	chr7	74228889	75131592	-470	FN	T	C	GT:BD:BK:BI:BVT:BLT:QQ	1|1:TP:gm:ti:SNP:homalt:39.9993	1/1:TP:gm:ti:SNP:homalt:39.9993	CommonFN			yes	no	Region in GTF2iRD2 that appears different in GRCh37 and 38, so that HG002 has a homozygous 195bp del relative to GRCh37 that causes low cov except ONT. Difficult to map and highly homozygous region, that has no haplotype partitioning for HiFi, but most variants except certain homopolymers appear to be supported by at least ONT and HiFi													1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:ti:SNP:homalt:30	1/1:TP:gm:ti:SNP:homalt:30	1|1:TP:gm:ti:SNP:homalt:33.9	1/1:TP:gm:ti:SNP:homalt:33.9	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	7:74228889	75131592
Common		GRCh37			7	chr7	74229359	75131122	-22	FN	A	G	GT:BD:BK:BI:BVT:BLT:QQ	1|1:TP:gm:ti:SNP:homalt:100	1/1:TP:gm:ti:SNP:homalt:100	CommonFN			yes	no	Region in GTF2iRD2 that appears different in GRCh37 and 38, so that HG002 has a homozygous 195bp del relative to GRCh37 that causes low cov except ONT. Difficult to map and highly homozygous region, that has no haplotype partitioning for HiFi, but most variants except certain homopolymers appear to be supported by at least ONT and HiFi													1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:ti:SNP:homalt:30	1/1:TP:gm:ti:SNP:homalt:30	1|1:TP:gm:ti:SNP:homalt:27.8	1/1:TP:gm:ti:SNP:homalt:27.8	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	7:74229359	75131122
Common		GRCh37			7	chr7	74229381	75131100	-529	FN	C	G	GT:BD:BK:BI:BVT:BLT:QQ	1|1:TP:gm:tv:SNP:homalt:39.9993	1/1:TP:gm:tv:SNP:homalt:39.9993	CommonFN			yes	no	Region in GTF2iRD2 that appears different in GRCh37 and 38, so that HG002 has a homozygous 195bp del relative to GRCh37 that causes low cov except ONT. Difficult to map and highly homozygous region, that has no haplotype partitioning for HiFi, but most variants except certain homopolymers appear to be supported by at least ONT and HiFi													1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:lm:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:tv:SNP:homalt:32.3	1/1:TP:gm:tv:SNP:homalt:32.3	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	7:74229381	75131100
Common		GRCh37			7	chr7	74229910	75130571	-141	FN	CG	C	GT:BD:BK:BI:BVT:BLT:QQ	1|1:TP:gm:d1_5:INDEL:homalt:33.9793	1/1:TP:gm:d1_5:INDEL:homalt:33.9793	CommonFN			yes	no	Region in GTF2iRD2 that appears different in GRCh37 and 38, so that HG002 has a homozygous 195bp del relative to GRCh37 that causes low cov except ONT. Difficult to map and highly homozygous region, that has no haplotype partitioning for HiFi, but most variants except certain homopolymers appear to be supported by at least ONT and HiFi													1|1:FN:lm:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:d1_5:INDEL:homalt:30	1/1:TP:gm:d1_5:INDEL:homalt:30	1|1:FN:lm:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	7:74229910	75130571
Common		GRCh37			7	chr7	74230052	75130430	-280	FN	G	A	GT:BD:BK:BI:BVT:BLT:QQ	1|1:TP:gm:ti:SNP:homalt:100	1/1:TP:gm:ti:SNP:homalt:100	CommonFN			yes	no	Region in GTF2iRD2 that appears different in GRCh37 and 38, so that HG002 has a homozygous 195bp del relative to GRCh37 that causes low cov except ONT. Difficult to map and highly homozygous region, that has no haplotype partitioning for HiFi, but most variants except certain homopolymers appear to be supported by at least ONT and HiFi													1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:ti:SNP:homalt:27.8	1/1:TP:gm:ti:SNP:homalt:27.8	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	7:74230052	75130430
Common		GRCh37			7	chr7	74230332	75130150	-5604	FN	GGAAA	G	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:.:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	Region in GTF2iRD2 that appears different in GRCh37 and 38, so that HG002 has a homozygous 195bp del relative to GRCh37 that causes low cov except ONT. Difficult to map and highly homozygous region, that has no haplotype partitioning for HiFi, but most variants except certain homopolymers appear to be supported by at least ONT and HiFi													1|1:FN:.:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:lm:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:lm:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:lm:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	7:74230332	75130150
NCBI	HG002_grch37_dipcall.vcf.gz	GRCh37	small-variants	SNP	7	chr7	74235923	75124546	-799	FP	T	A	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:.:tv:SNP:het	yes	no	segdup region	yes	no	Region in GTF2iRD2 that appears different in GRCh37 and 38, so that HG002 has a homozygous 195bp del relative to GRCh37 that causes low cov except ONT. Difficult to map and highly homozygous region, that has no haplotype partitioning for HiFi, but most variants except certain homopolymers appear to be supported by at least ONT and HiFi																											7:74235923	75124546
NCBI	HG002_grch37_dipcall.vcf.gz	GRCh37	small-variants	SNP	7	chr7	74236723	75123747	-295071	FP_FN	C	T	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:ti:SNP:homalt	0/1:FP:am:30:ti:SNP:het	yes	no	evidence for HOM; segdup region	yes	no	Region in GTF2iRD2 that appears different in GRCh37 and 38, so that HG002 has a homozygous 195bp del relative to GRCh37 that causes low cov except ONT. Difficult to map and highly homozygous region, that has no haplotype partitioning for HiFi, but most variants except certain homopolymers appear to be supported by at least ONT and HiFi																											7:74236723	75123747
Common		GRCh37			7	chr7	74243785	74828676	0	FN	G	GAA	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:100:i1_5:INDEL:homalt	1/1:TP:gm:100:i1_5:INDEL:homalt	CommonFN			unsure	unsure	low coverage except HiFi and ONT, and HiFi reads are a bit noisy and not haplotype-partitioned in highly homozygous region													1|1:TP:gm:452.73:i1_5:INDEL:homalt	1/1:TP:gm:452.73:i1_5:INDEL:homalt	1|1:FN:.:.:i1_5:INDEL:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:am:.:i1_5:INDEL:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:i1_5:INDEL:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:i1_5:INDEL:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:i1_5:INDEL:homalt	.:.:.:0:.:NOCALL:nocall	1|1:TP:gm:2:i1_5:INDEL:homalt	1/1:TP:gm:2:i1_5:INDEL:homalt	7:74243785	74828676
Common		GRCh38			7	chr7	74243785	74828676	1274	FN	G	GAA	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	CommonFN			unsure	unsure	low coverage except HiFi and ONT, and HiFi reads are a bit noisy and not haplotype-partitioned in highly homozygous region													1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:i1_5:INDEL:homalt:63.25	1/1:TP:gm:i1_5:INDEL:homalt:63.25	1|1:FN:am:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:i1_5:INDEL:homalt:0	1/1:TP:gm:i1_5:INDEL:homalt:0	1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:i1_5:INDEL:homalt:3	1/1:TP:gm:i1_5:INDEL:homalt:3		74243785
NCBI	HG002_grch38_dipcall.vcf.gz	GRCh38	small-variants	SNP	7	chr7	74245071	74829950	1323	FP	G	A	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:.:ti:SNP:het	yes	no	segdup region	yes	no	Difficult to map and highly homozygous region, that has no haplotype partitioning for HiFi, but most variants except certain homopolymers appear to be supported by at least ONT and HiFi				skip																								74245071
NCBI	HG002_grch38_dipcall.vcf.gz	GRCh38	small-variants	INDEL	7	chr7	74246394	74831273	134	FP	T	TTATC	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:.:i1_5:INDEL:het	yes	no	segdup region	yes	no	Difficult to map and highly homozygous region, that has no haplotype partitioning for HiFi, but most variants except certain homopolymers appear to be supported by at least ONT and HiFi				skip																								74246394
NCBI	HG002_grch38_dipcall.vcf.gz	GRCh38	small-variants	INDEL	7	chr7	74246528	74831407	1802	FP	CCTAT	C	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:.:d1_5:INDEL:het	yes	no	segdup region	yes	no	Difficult to map and highly homozygous region, that has no haplotype partitioning for HiFi, but most variants except certain homopolymers appear to be supported by at least ONT and HiFi				skip																								74246528
Common		GRCh38			7	chr7	74248332	74833209	12	FN	C	T	GT:BD:BK:QQ:BI:BVT:BLT	1|0:TP:gm:12.4579:ti:SNP:het	0/1:TP:gm:12.4579:ti:SNP:het	CommonFN			yes	no	Difficult to map and highly homozygous region, that has no haplotype partitioning for HiFi, but most variants except certain homopolymers appear to be supported by at least ONT and HiFi													1|0:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	1|0:FN:lm:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	1|0:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	1|0:TP:gm:8.8:ti:SNP:het	0/1:TP:gm:8.8:ti:SNP:het	1|0:FN:lm:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	1|0:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	1|0:FN:lm:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall		74248332
Common		GRCh38			7	chr7	74248344	74833221	2528	FN	TTGTGTG	T,TTGTGTGTGTGTG	GT:BD:BK:BI:BVT:BLT:QQ	1|2:FN:lm:d6_15,i6_15:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes		likely correct for both haplotypes given HiFi and ONT support but is a bit noisy and low coverage													1|2:FN:.:d6_15,i6_15:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:0	1|2:FN:am:d6_15,i6_15:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:1689.73	1|2:FN:.:d6_15,i6_15:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:0	1|2:FN:lm:d6_15,i6_15:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:0	1|2:FN:am:d6_15,i6_15:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:0	1|2:FN:.:d6_15,i6_15:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:0	1|2:FN:lm:d6_15,i6_15:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:16		74248344
Common		GRCh37			7	chr7	74250873	74835749	400	FN	A	G	GT:BD:BK:BI:BVT:BLT:QQ	1|1:TP:gm:ti:SNP:homalt:39.9993	1/1:TP:gm:ti:SNP:homalt:39.9993	CommonFN			yes	no	Difficult to map and highly homozygous region, that has no haplotype partitioning for HiFi, but most variants except certain homopolymers appear to be supported by at least ONT and HiFi													1|1:TP:gm:ti:SNP:homalt:183.78	1/1:TP:gm:ti:SNP:homalt:183.78	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:ti:SNP:homalt:37.3	1/1:TP:gm:ti:SNP:homalt:37.3	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	7:74250873	74835749
Common		GRCh37			7	chr7	74251271	74836149	613	FN	C	T	GT:BD:BK:BI:BVT:BLT:QQ	1|1:TP:gm:ti:SNP:homalt:100	1/1:TP:gm:ti:SNP:homalt:100	CommonFN			yes	no	Difficult to map and highly homozygous region, that has no haplotype partitioning for HiFi, but most variants except certain homopolymers appear to be supported by at least ONT and HiFi													1|1:TP:gm:ti:SNP:homalt:209.78	1/1:TP:gm:ti:SNP:homalt:209.78	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:ti:SNP:homalt:41.3	1/1:TP:gm:ti:SNP:homalt:41.3	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	7:74251271	74836149
Common		GRCh37			7	chr7	74251884	74836762	994	FN	C	T	GT:BD:BK:BI:BVT:BLT:QQ	1|1:TP:gm:ti:SNP:homalt:100	1/1:TP:gm:ti:SNP:homalt:100	CommonFN			yes	no	Difficult to map and highly homozygous region, that has no haplotype partitioning for HiFi, but most variants except certain homopolymers appear to be supported by at least ONT and HiFi													1|1:TP:gm:ti:SNP:homalt:125.84	1/1:TP:gm:ti:SNP:homalt:125.84	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:ti:SNP:homalt:38.7	1/1:TP:gm:ti:SNP:homalt:38.7	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	7:74251884	74836762
Common		GRCh37			7	chr7	74252878	74837756	1261	FN	C	CT	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:100:i1_5:INDEL:homalt	1/1:TP:gm:100:i1_5:INDEL:homalt	CommonFN			yes	no	Difficult to map and highly homozygous region, that has no haplotype partitioning for HiFi, but most variants except certain homopolymers appear to be supported by at least ONT and HiFi													1|1:TP:gm:30.25:i1_5:INDEL:homalt	1/1:TP:gm:30.25:i1_5:INDEL:homalt	1|1:FN:.:.:i1_5:INDEL:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:i1_5:INDEL:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:i1_5:INDEL:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:i1_5:INDEL:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:i1_5:INDEL:homalt	.:.:.:0:.:NOCALL:nocall	1|1:TP:gm:3:i1_5:INDEL:homalt	1/1:TP:gm:3:i1_5:INDEL:homalt	7:74252878	74837756
Common		GRCh38			7	chr7	74254137	74839017	262533	FN	C	T	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:100:ti:SNP:homalt	1/1:TP:gm:100:ti:SNP:homalt	CommonFN			yes	no	Difficult to map and highly homozygous region, that has no haplotype partitioning for HiFi, but most variants except certain homopolymers appear to be supported by at least ONT and HiFi													1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:TP:gm:27.2:ti:SNP:homalt	1/1:TP:gm:27.2:ti:SNP:homalt	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall		74254137
Common		GRCh37			7	chr7	74258915	75101550	-28	FN	C	A	GT:BD:BK:QQ:BI:BVT:BLT	0|1:FN:lm:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall	CommonFN			yes	no	Difficult to map and highly homozygous region, that has no haplotype partitioning for HiFi, but most variants except certain homopolymers appear to be supported by at least ONT and HiFi													0|1:FN:.:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:TP:gm:64.77:tv:SNP:het	0/1:TP:gm:64.77:tv:SNP:het	0|1:FN:.:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:TP:gm:27.2:tv:SNP:het	0/1:TP:gm:27.2:tv:SNP:het	0|1:FN:.:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:.:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:TP:gm:2:tv:SNP:het	0/1:TP:gm:2:tv:SNP:het	7:74258915	75101550
Common		GRCh37			7	chr7	74258943	75101522	-758	FN	A	G	GT:BD:BK:BI:BVT:BLT:QQ	0|1:TP:gm:ti:SNP:het:5.7125	0/1:TP:gm:ti:SNP:het:5.7125	CommonFN			yes	no	Difficult to map and highly homozygous region, that has no haplotype partitioning for HiFi, but most variants except certain homopolymers appear to be supported by at least ONT and HiFi													0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:TP:gm:ti:SNP:het:61.77	0/1:TP:gm:ti:SNP:het:61.77	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:TP:gm:ti:SNP:het:24.7	0/1:TP:gm:ti:SNP:het:24.7	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	7:74258943	75101522
Common		GRCh37			7	chr7	74259701	75100764	-4324	FN	A	G	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:100:ti:SNP:homalt	1/1:TP:gm:100:ti:SNP:homalt	CommonFN			yes	no	Difficult to map and highly homozygous region, that has no haplotype partitioning for HiFi, but most variants except certain homopolymers appear to be supported by at least ONT and HiFi													1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:TP:gm:29.2:ti:SNP:homalt	1/1:TP:gm:29.2:ti:SNP:homalt	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:TP:gm:35:ti:SNP:homalt	1/1:TP:gm:35:ti:SNP:homalt	7:74259701	75100764
Common		GRCh37			7	chr7	74264022	75096440	-244935	FN	C	CA	GT:BD:BK:BI:BVT:BLT:QQ	1|1:TP:gm:i1_5:INDEL:homalt:29.2095	1/1:TP:gm:i1_5:INDEL:homalt:29.2095	CommonFN			unsure	unsure	Difficult to map and highly homozygous region, that has no haplotype partitioning for HiFi, but most variants except certain homopolymers appear to be supported by at least ONT and HiFi													1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	7:74264022	75096440
Common		GRCh38			7	chr7	74508418	74851505	-52	FN	A	G	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	Difficult to map and highly homozygous region, that has no haplotype partitioning for HiFi, but most variants except certain homopolymers appear to be supported by at least ONT and HiFi													1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:ti:SNP:homalt:32.9	1/1:TP:gm:ti:SNP:homalt:32.9	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0		74508418
Common		GRCh38			7	chr7	74508470	74851453	-119	FN	A	G	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	Difficult to map and highly homozygous region, that has no haplotype partitioning for HiFi, but most variants except certain homopolymers appear to be supported by at least ONT and HiFi													1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:ti:SNP:homalt:40	1/1:TP:gm:ti:SNP:homalt:40	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0		74508470
Roche	RN_HG002_Illumina_PacBio_Oxford.vcf.gz	GRCh38	small-variants	INDEL	7	chr7	74508598	74851334	0	FN	T	TGGCGGCGTC	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:.:i6_15:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0 	yes	no		yes	no	Difficult to map and highly homozygous region, that has no haplotype partitioning for HiFi, but most variants except certain homopolymers appear to be supported by at least ONT and HiFi				skip																								74508598
Common		GRCh38			7	chr7	74508598	74851334	-244	FN	T	TGGCGGCGTC	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:.:i6_15:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	Difficult to map and highly homozygous region, that has no haplotype partitioning for HiFi, but most variants except certain homopolymers appear to be supported by at least ONT and HiFi													1|1:FN:.:i6_15:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:i6_15:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:i6_15:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:i6_15:INDEL:homalt:26.5	1/1:TP:gm:i6_15:INDEL:homalt:26.5	1|1:FN:.:i6_15:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:i6_15:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:i6_15:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0		74508598
Common		GRCh38			7	chr7	74508842	74851090	-481	FN	T	C	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	Difficult to map and highly homozygous region, that has no haplotype partitioning for HiFi, but most variants except certain homopolymers appear to be supported by at least ONT and HiFi													1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:ti:SNP:homalt:41.4	1/1:TP:gm:ti:SNP:homalt:41.4	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0		74508842
Common		GRCh38			7	chr7	74509323	74850609	-102	FN	A	G	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:17.7907:ti:SNP:homalt	1/1:TP:gm:17.7907:ti:SNP:homalt	CommonFN			yes	no	Difficult to map and highly homozygous region, that has no haplotype partitioning for HiFi, but most variants except certain homopolymers appear to be supported by at least ONT and HiFi													1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:TP:gm:38.2:ti:SNP:homalt	1/1:TP:gm:38.2:ti:SNP:homalt	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall		74509323
Common		GRCh38			7	chr7	74509425	74850507	-1530	FN	A	G	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:100:ti:SNP:homalt	1/1:TP:gm:100:ti:SNP:homalt	CommonFN			yes	no	Difficult to map and highly homozygous region, that has no haplotype partitioning for HiFi, but most variants except certain homopolymers appear to be supported by at least ONT and HiFi													1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:TP:gm:41.9:ti:SNP:homalt	1/1:TP:gm:41.9:ti:SNP:homalt	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall		74509425
NCBI	HG002_grch38_dipcall.vcf.gz	GRCh38	small-variants	SNP	7	chr7	74510955	74848977	-1100	FN	C	T	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	yes	no	segdup region	yes	no	Difficult to map and highly homozygous region, that has no haplotype partitioning for HiFi, but most variants except certain homopolymers appear to be supported by at least ONT and HiFi				skip																								74510955
Common		GRCh38			7	chr7	74512055	74847877	-454	FN	A	C	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	Difficult to map and highly homozygous region, that has no haplotype partitioning for HiFi, but most variants except certain homopolymers appear to be supported by at least ONT and HiFi													1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0		74512055
Common		GRCh38			7	chr7	74512509	74847423	-28	FN	C	T	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:100:ti:SNP:homalt	1/1:TP:gm:100:ti:SNP:homalt	CommonFN			yes	no	Difficult to map and highly homozygous region, that has no haplotype partitioning for HiFi, but most variants except certain homopolymers appear to be supported by at least ONT and HiFi													1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:TP:gm:57:ti:SNP:homalt	1/1:TP:gm:57:ti:SNP:homalt	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall		74512509
Common		GRCh38			7	chr7	74512537	74847395	-8	FN	A	G	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:31.5498:ti:SNP:homalt	1/1:TP:gm:31.5498:ti:SNP:homalt	CommonFN			yes	no	Difficult to map and highly homozygous region, that has no haplotype partitioning for HiFi, but most variants except certain homopolymers appear to be supported by at least ONT and HiFi													1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:TP:gm:42.1:ti:SNP:homalt	1/1:TP:gm:42.1:ti:SNP:homalt	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall		74512537
Common		GRCh38			7	chr7	74512545	74847387	-900	FN	G	T	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:27.6974:tv:SNP:homalt	1/1:TP:gm:27.6974:tv:SNP:homalt	CommonFN			yes	no	Difficult to map and highly homozygous region, that has no haplotype partitioning for HiFi, but most variants except certain homopolymers appear to be supported by at least ONT and HiFi													1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:TP:gm:38.1:tv:SNP:homalt	1/1:TP:gm:38.1:tv:SNP:homalt	1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall		74512545
Common		GRCh38			7	chr7	74513445	74846487	-2205	FN	T	C	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	Difficult to map and highly homozygous region, that has no haplotype partitioning for HiFi, but most variants except certain homopolymers appear to be supported by at least ONT and HiFi													1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:ti:SNP:homalt:45.9	1/1:TP:gm:ti:SNP:homalt:45.9	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0		74513445
Common		GRCh38			7	chr7	74515649	74844282	-601	FN	T	A	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:12.6773:tv:SNP:homalt	1/1:TP:gm:12.6773:tv:SNP:homalt	CommonFN			yes	no	Difficult to map and highly homozygous region, that has no haplotype partitioning for HiFi, but most variants except certain homopolymers appear to be supported by at least ONT and HiFi													1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:TP:gm:39.5:tv:SNP:homalt	1/1:TP:gm:39.5:tv:SNP:homalt	1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall		74515649
Common		GRCh38			7	chr7	74516251	74843681	-940	FN	A	G	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:100:ti:SNP:homalt	1/1:TP:gm:100:ti:SNP:homalt	CommonFN			yes	no	Difficult to map and highly homozygous region, that has no haplotype partitioning for HiFi, but most variants except certain homopolymers appear to be supported by at least ONT and HiFi													1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:TP:gm:43.2:ti:SNP:homalt	1/1:TP:gm:43.2:ti:SNP:homalt	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall		74516251
Common		GRCh38			7	chr7	74517191	74842741	-122	FN	A	G	GT:BD:BK:QQ:BI:BVT:BLT	0|1:TP:gm:8.4968:ti:SNP:het	0/1:TP:gm:8.4968:ti:SNP:het	CommonFN			yes	no	Difficult to map and highly homozygous region, that has no haplotype partitioning for HiFi, but most variants except certain homopolymers appear to be supported by at least ONT and HiFi													0|1:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:TP:gm:22.8:ti:SNP:het	0/1:TP:gm:22.8:ti:SNP:het	0|1:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:TP:gm:4:ti:SNP:het	0/1:TP:gm:4:ti:SNP:het		74517191
Common		GRCh38			7	chr7	74517313	74842619	-28	FN	A	G	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:lm:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	Difficult to map and highly homozygous region, that has no haplotype partitioning for HiFi, but most variants except certain homopolymers appear to be supported by at least ONT and HiFi													0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:TP:gm:ti:SNP:het:12.6	0/1:TP:gm:ti:SNP:het:12.6	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0		74517313
Common		GRCh38			7	chr7	74517341	74842591	-154	FN	C	A	GT:BD:BK:QQ:BI:BVT:BLT	0|1:TP:gm:14.5541:tv:SNP:het	0/1:TP:gm:14.5541:tv:SNP:het	CommonFN			yes	no	Difficult to map and highly homozygous region, that has no haplotype partitioning for HiFi, but most variants except certain homopolymers appear to be supported by at least ONT and HiFi													0|1:FN:.:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:.:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:.:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:TP:gm:4.9:tv:SNP:het	0/1:TP:gm:4.9:tv:SNP:het	0|1:FN:.:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:.:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:TP:gm:2:tv:SNP:het	0/1:TP:gm:2:tv:SNP:het		74517341
Common		GRCh38			7	chr7	74517495	74842437	-3133	FN	T	C	GT:BD:BK:QQ:BI:BVT:BLT	0|1:TP:gm:24.0936:ti:SNP:het	0/1:TP:gm:24.0936:ti:SNP:het	CommonFN			yes	no	Difficult to map and highly homozygous region, that has no haplotype partitioning for HiFi, but most variants except certain homopolymers appear to be supported by at least ONT and HiFi													0|1:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:TP:gm:10.8:ti:SNP:het	0/1:TP:gm:10.8:ti:SNP:het	0|1:TP:gm:0:ti:SNP:het	0/1:TP:gm:0:ti:SNP:het	0|1:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall		74517495
Common		GRCh38			7	chr7	74520628	74839304	-11474	FN	T	C	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:100:ti:SNP:homalt	1/1:TP:gm:100:ti:SNP:homalt	CommonFN			yes	no	Difficult to map and highly homozygous region, that has no haplotype partitioning for HiFi, but most variants except certain homopolymers appear to be supported by at least ONT and HiFi													1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:TP:gm:25.8:ti:SNP:homalt	1/1:TP:gm:25.8:ti:SNP:homalt	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall		74520628
Roche	RN_HG002_Illumina_PacBio_Oxford.vcf.gz	GRCh38	small-variants	INDEL	7	chr7	74533902	74827830	-2028	FN	C	CT	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0 	yes	no		unsure	unsure	low coverage except HiFi and ONT, and HiFi reads are a bit noisy and not haplotype-partitioned in highly homozygous region				skip																								74533902
Roche	RN_HG002_Illumina_PacBio_Oxford.vcf.gz	GRCh38	small-variants	INDEL	7	chr7	74535943	74825802	-911	FP_FN	CT	C	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:100:d1_5:INDEL:het 	yes	no		unsure	unsure	low coverage except HiFi and ONT, and HiFi reads are a bit noisy and not haplotype-partitioned in highly homozygous region				skip																								74535943
CMH_DRAGEN_3.6.3	NA24385.hard-filtered.vcf.gz	GRCh38	small-variants	INDEL	7	chr7	74536856	74824891	-131	FN	C	CAA	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	yes	no		unsure	unsure	low coverage except HiFi and ONT, and HiFi reads are a bit noisy and not haplotype-partitioned in highly homozygous region				skip																								74536856
Common		GRCh38			7	chr7	74536987	74824760	-6339	FN	C	T	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:29.5872:ti:SNP:homalt	1/1:TP:gm:29.5872:ti:SNP:homalt	CommonFN			yes	no	Difficult to map and highly homozygous region, that has no haplotype partitioning for HiFi, but most variants except certain homopolymers appear to be supported by at least ONT and HiFi													1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:TP:gm:30:ti:SNP:homalt	1/1:TP:gm:30:ti:SNP:homalt	1|1:TP:gm:18.9:ti:SNP:homalt	1/1:TP:gm:18.9:ti:SNP:homalt	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall		74536987
NCBI	HG002_grch38_dipcall.vcf.gz	GRCh38	small-variants	INDEL	7	chr7	74543337	74818421	-2624	FP	A	AT	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:.:i1_5:INDEL:het	yes	no	segdup region	yes	no	Difficult to map and highly homozygous region, that has no haplotype partitioning for HiFi, but most variants except certain homopolymers appear to be supported by at least ONT and HiFi				skip																								74543337
Common		GRCh38			7	chr7	74545963	74815797	-280	FN	GGAAAGAAAGAAA	G	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:lm:d6_15:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no		benchmark likely missing ~20bp del in other haplotype due to highly homozygous region													1|1:FN:.:d6_15:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:d6_15:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:lm:d6_15:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:d6_15:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:d6_15:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:d6_15:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:d6_15:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0		74545963
NYGC	HG-002-2x250-b38.recalibrated.haplotypeCalls.vcf.gz	GRCh38	small-variants	SNP	7	chr7	74546243	74815517	-142	FP_FN	G	A	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:ti:SNP:homalt	0/1:FP:am:51.77:ti:SNP:het 	yes	yes		yes	no	Difficult to map and highly homozygous region, that has no haplotype partitioning for HiFi, but most variants except certain homopolymers appear to be supported by at least ONT and HiFi																												74546243
Common		GRCh38			7	chr7	74546384	74815375	-9	FN	CG	C	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:100:d1_5:INDEL:homalt	1/1:TP:gm:100:d1_5:INDEL:homalt	CommonFN			unsure	unsure	little coverage except HiFi and ONT, and HiFi reads are a bit noisy and not haplotype-partitioned in highly homozygous region													1|1:FN:.:.:d1_5:INDEL:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:d1_5:INDEL:homalt	.:.:.:0:.:NOCALL:nocall	1|1:TP:gm:30:d1_5:INDEL:homalt	1/1:TP:gm:30:d1_5:INDEL:homalt	1|1:FN:lm:.:d1_5:INDEL:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:d1_5:INDEL:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:d1_5:INDEL:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:d1_5:INDEL:homalt	.:.:.:0:.:NOCALL:nocall		74546384
Common		GRCh38			7	chr7	74546393	74815366	-520	FN	G	A	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:36.989:ti:SNP:homalt	1/1:TP:gm:36.989:ti:SNP:homalt	CommonFN			yes	no	Difficult to map and highly homozygous region, that has no haplotype partitioning for HiFi, but most variants except certain homopolymers appear to be supported by at least ONT and HiFi													1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:TP:gm:30:ti:SNP:homalt	1/1:TP:gm:30:ti:SNP:homalt	1|1:TP:gm:7.9:ti:SNP:homalt	1/1:TP:gm:7.9:ti:SNP:homalt	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall		74546393
Common		GRCh38			7	chr7	74546913	74814846	-1487	FN	C	G	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	Difficult to map and highly homozygous region, that has no haplotype partitioning for HiFi, but most variants except certain homopolymers appear to be supported by at least ONT and HiFi													1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:tv:SNP:homalt:16.3	1/1:TP:gm:tv:SNP:homalt:16.3	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0		74546913
Common		GRCh38			7	chr7	74548400	74813359	-218	FN	T	C	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:100:ti:SNP:homalt	1/1:TP:gm:100:ti:SNP:homalt	CommonFN			yes	no	Difficult to map and highly homozygous region, that has no haplotype partitioning for HiFi, but most variants except certain homopolymers appear to be supported by at least ONT and HiFi													1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:TP:gm:30:ti:SNP:homalt	1/1:TP:gm:30:ti:SNP:homalt	1|1:TP:gm:15:ti:SNP:homalt	1/1:TP:gm:15:ti:SNP:homalt	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall		74548400
Common		GRCh38			7	chr7	74548618	74813141	-23	FN	G	A	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:lm:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	Difficult to map and highly homozygous region, that has no haplotype partitioning for HiFi, but most variants except certain homopolymers appear to be supported by at least ONT and HiFi													1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:ti:SNP:homalt:14.2	1/1:TP:gm:ti:SNP:homalt:14.2	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0		74548618
Common		GRCh38			7	chr7	74548641	74813118	-491	FN	C	T	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:21.6804:ti:SNP:homalt	1/1:TP:gm:21.6804:ti:SNP:homalt	CommonFN			yes	no	Difficult to map and highly homozygous region, that has no haplotype partitioning for HiFi, but most variants except certain homopolymers appear to be supported by at least ONT and HiFi													1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:TP:gm:12.3:ti:SNP:homalt	1/1:TP:gm:12.3:ti:SNP:homalt	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall		74548641
Common		GRCh38			7	chr7	74549132	74812627	-67	FN	A	T	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:100:tv:SNP:homalt	1/1:TP:gm:100:tv:SNP:homalt	CommonFN			yes	no	Difficult to map and highly homozygous region, that has no haplotype partitioning for HiFi, but most variants except certain homopolymers appear to be supported by at least ONT and HiFi													1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:TP:gm:30:tv:SNP:homalt	1/1:TP:gm:30:tv:SNP:homalt	1|1:TP:gm:14.6:tv:SNP:homalt	1/1:TP:gm:14.6:tv:SNP:homalt	1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall		74549132
Common		GRCh38			7	chr7	74549199	74812560	-282	FN	G	A	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:39.9993:ti:SNP:homalt	1/1:TP:gm:39.9993:ti:SNP:homalt	CommonFN			yes	no	Difficult to map and highly homozygous region, that has no haplotype partitioning for HiFi, but most variants except certain homopolymers appear to be supported by at least ONT and HiFi													1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:TP:gm:30:ti:SNP:homalt	1/1:TP:gm:30:ti:SNP:homalt	1|1:TP:gm:15.5:ti:SNP:homalt	1/1:TP:gm:15.5:ti:SNP:homalt	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall		74549199
Common		GRCh38			7	chr7	74549483	74812278	-1177	FN	G	C	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	Difficult to map and highly homozygous region, that has no haplotype partitioning for HiFi, but most variants except certain homopolymers appear to be supported by at least ONT and HiFi													1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0		74549483
Common		GRCh38			7	chr7	74550662	74811101	-57	FN	G	A	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:100:ti:SNP:homalt	1/1:TP:gm:100:ti:SNP:homalt	CommonFN			yes	no	Difficult to map and highly homozygous region, that has no haplotype partitioning for HiFi, but most variants except certain homopolymers appear to be supported by at least ONT and HiFi													1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:lm:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:TP:gm:14.6:ti:SNP:homalt	1/1:TP:gm:14.6:ti:SNP:homalt	1|1:TP:gm:0:ti:SNP:homalt	1/1:TP:gm:0:ti:SNP:homalt	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall		74550662
Common		GRCh38			7	chr7	74550719	74811044	-237	FN	A	G	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:100:ti:SNP:homalt	1/1:TP:gm:100:ti:SNP:homalt	CommonFN			yes	no	Difficult to map and highly homozygous region, that has no haplotype partitioning for HiFi, but most variants except certain homopolymers appear to be supported by at least ONT and HiFi													1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:TP:gm:7:ti:SNP:homalt	1/1:TP:gm:7:ti:SNP:homalt	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall		74550719
Common		GRCh38			7	chr7	74550955	74810807	-208	FN	GA	G	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:.:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	Difficult to map and highly homozygous region, that has no haplotype partitioning for HiFi, but most variants except certain homopolymers appear to be supported by at least ONT and HiFi													1|1:FN:.:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:d1_5:INDEL:homalt:30	1/1:TP:gm:d1_5:INDEL:homalt:30	1|1:FN:.:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:lm:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0		74550955
Common		GRCh38			7	chr7	74551163	74810599	-818	FN	A	G	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:100:ti:SNP:homalt	1/1:TP:gm:100:ti:SNP:homalt	CommonFN			yes	no	Difficult to map and highly homozygous region, that has no haplotype partitioning for HiFi, but most variants except certain homopolymers appear to be supported by at least ONT and HiFi													1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:TP:gm:30:ti:SNP:homalt	1/1:TP:gm:30:ti:SNP:homalt	1|1:TP:gm:7.1:ti:SNP:homalt	1/1:TP:gm:7.1:ti:SNP:homalt	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall		74551163
BCM-HGSC_xAtlas	HG002.GRCh38.60x.1_merged.vcf.gz	GRCh38	small-variants	INDEL	7	chr7	74551981	74809781	0	FN	T	TTTA	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0 	Yes	No		yes	no	Difficult to map and highly homozygous region, that has no haplotype partitioning for HiFi, but most variants except certain homopolymers appear to be supported by at least ONT and HiFi				skip																								74551981
Common		GRCh38			7	chr7	74551981	74809781	-140	FN	T	TTTA	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	Difficult to map and highly homozygous region, that has no haplotype partitioning for HiFi, but most variants except certain homopolymers appear to be supported by at least ONT and HiFi													1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:i1_5:INDEL:homalt:30	1/1:TP:gm:i1_5:INDEL:homalt:30	1|1:TP:gm:i1_5:INDEL:homalt:13.1	1/1:TP:gm:i1_5:INDEL:homalt:13.1	1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0		74551981
CMH_DRAGEN_3.6.3	NA24385.hard-filtered.vcf.gz	GRCh38	small-variants	INDEL	7	chr7	74552124	74809641	0	FN	C	CA	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	yes	no		yes	no	Difficult to map and highly homozygous region, that has no haplotype partitioning for HiFi, but most variants except certain homopolymers appear to be supported by at least ONT and HiFi				skip																								74552124
Common		GRCh38			7	chr7	74552124	74809641	25938950	FN	C	CA	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:36.9903:i1_5:INDEL:homalt	1/1:TP:gm:36.9903:i1_5:INDEL:homalt	CommonFN			yes	no	Difficult to map and highly homozygous region, that has no haplotype partitioning for HiFi, but most variants except certain homopolymers appear to be supported by at least ONT and HiFi													1|1:FN:.:.:i1_5:INDEL:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:i1_5:INDEL:homalt	.:.:.:0:.:NOCALL:nocall	1|1:TP:gm:30:i1_5:INDEL:homalt	1/1:TP:gm:30:i1_5:INDEL:homalt	1|1:FN:.:.:i1_5:INDEL:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:lm:.:i1_5:INDEL:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:i1_5:INDEL:homalt	.:.:.:0:.:NOCALL:nocall	1|1:TP:gm:7:i1_5:INDEL:homalt	1/1:TP:gm:7:i1_5:INDEL:homalt		74552124
Common		GRCh37			7	chr7	100346214	100748591	0	FN	G	GT	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no	yes	Homopolymer error due to noisy HiFi reads in fairly short homopolymer													0|1:TP:gm:i1_5:INDEL:het:43.73	0/1:TP:gm:i1_5:INDEL:het:43.73	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	7:100346214	100748591
Roche	RN_HG002_Illumina_PacBio_Oxford.vcf.gz	GRCh38	small-variants	INDEL	7	chr7	100346214	100748591	0	FN	G	GT	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0 	unsure	unsure	not in Illimina, only in few PacBio reads	no	yes	Homopolymer error due to noisy HiFi reads in fairly short homopolymer																												100346214
Common		GRCh38			7	chr7	100346214	100748591	208	FN	G	GT	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no	yes	Homopolymer error due to noisy HiFi reads in fairly short homopolymer													0|1:TP:gm:i1_5:INDEL:het:43.73	0/1:TP:gm:i1_5:INDEL:het:43.73	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0		100346214
Common		GRCh37			7	chr7	100346422	100748799	0	FN	CG	C	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no	yes	likely hifiasm consensus error since no support across techs													0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	7:100346422	100748799
Common		GRCh38			7	chr7	100346422	100748799	853	FN	CG	C	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no	yes	likely hifiasm consensus error since no support across techs													0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0		100346422
Common		GRCh37			7	chr7	100347275	100749652	1	FN	ATAT	AAT,*	GT:BD:BK:BI:BVT:BLT:QQ	2|1:FN:lm:c1_5,d1_5:INDEL:hetalt:.	0/1:TP:gm:d1_5:INDEL:het:36.9897	CommonFN			no	yes	hifiasm is correct in adjacent homopolymer and TR except for del in place of SNV													2|1:FN:lm:c1_5,d1_5:INDEL:hetalt:.	0/1:TP:gm:d1_5:INDEL:het:604.73	2|1:FN:lm:c1_5,d1_5:INDEL:hetalt:.	0/1:TP:gm:d1_5:INDEL:het:292.73	2|1:FN:lm:c1_5,d1_5:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:0	2|1:FN:am:c1_5,d1_5:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:0	2|1:FN:lm:c1_5,d1_5:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:0	2|1:TP:gm:c1_5,d1_5:INDEL:hetalt:31.7	0/1:TP:gm:d1_5:INDEL:het:31.7	2|1:FN:lm:c1_5,d1_5:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:0	7:100347275	100749652
Common		GRCh37			7	chr7	100347276	100749653	2770	FP	T	A	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:36.989:FP:lm:tv:SNP:het	CommonFP			no	yes	hifiasm is correct in adjacent homopolymer and TR except for del in place of SNV													.:.:.:.:.:NOCALL:nocall	0/1:1063.77:FP:lm:tv:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:599.77:FP:lm:tv:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:lm:tv:SNP:het	.:.:.:.:.:NOCALL:nocall	1/1:326.01:FP:lm:tv:SNP:homalt	.:.:.:.:.:NOCALL:nocall	1/1:0:FP:lm:tv:SNP:homalt	.:.:.:.:.:NOCALL:nocall	0/1:50:FP:lm:tv:SNP:het	.:.:.:.:.:NOCALL:nocall	1/1:28:FP:lm:tv:SNP:homalt	7:100347276	100749653
DNAnexus	GRCh38_HG002_WGS_union.vcf.gz	GRCh38	small-variants	SNP	7	chr7	100350046	100752423	29229	FP	T	C	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:.:ti:SNP:het 	yes	no	10x -  strong CT het,  Other tech show TT no variant, Illumina and 10x genomics data both shown heterozygous, but both long read technolgies (PacBio and ONT) show homozygous reference. Because this is repeat region, we will take long reads' information for variant calling.  							skip																								100350046
PacBio_gatk4	gatk4hc_HG002_15kb_20kb_53X_SequelII.vcf.gz	GRCh38	small-variants	INDEL	7	chr7	100379274	100781652	6213	FP_FN	C	CT	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:91:i1_5:INDEL:het	yes	no								skip																								100379274
CMH_DRAGEN_3.6.3	NA24385.hard-filtered.vcf.gz	GRCh37	small-variants	INDEL	7	chr7	100385487	100787865	0	FP	TCTCA	T	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:50:FP:.:d1_5:INDEL:het	unsure	unsure	Query is somewhat well supported by aligments but not sure due to allele inconsistencies of reads with same haplotag. ONT looks like the  best supporting long reads for the query.	no	yes	Likely an error in hifiasm in TR due to region of high homozygosity																											7:100385487	100787865
Common		GRCh37			7	chr7	100385487	100787865	0	FP	TCTCA	T	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:.:d1_5:INDEL:het	CommonFP			no	yes	Likely an error in hifiasm in TR due to region of high homozygosity													.:.:.:.:.:NOCALL:nocall	0/1:565.73:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:1296.73:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:670.6:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:50:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:14:FP:.:d1_5:INDEL:het	7:100385487	100787865
PacBio_gatk4	gatk4hc_HG002_15kb_20kb_53X_SequelII.vcf.gz	GRCh38	small-variants	INDEL	7	chr7	100385487	100787865	0	FP	TCTCA	T	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:565.73:FP:.:d1_5:INDEL:het	unsure	unsure	deletion present in all pileups, but all have higher coverage than expected	no	yes	Likely an error in hifiasm in TR due to region of high homozygosity																												100385487
Common		GRCh38			7	chr7	100385487	100787865	40016541	FP	TCTCA	T	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:.:d1_5:INDEL:het	CommonFP			no	yes	Likely an error in hifiasm in TR due to region of high homozygosity													.:.:.:.:.:NOCALL:nocall	0/1:565.73:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:1298.73:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:859.6:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:50:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:14:FP:.:d1_5:INDEL:het		100385487
DNAnexus	hs37d5_HG002_WGS_union.vcf.gz	GRCh37	small-variants	INDEL	7	chr7	140504206	140804406	0	FP_FN	T	TG	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:0:i1_5:INDEL:het	unsure	no	This is right next to a homopolymer region (10 G's in with one T the reference) The benchmark set (by PacBio) looks more correct than the query callset. However, ONT reads are suggesting mutlipe other complicated possibilities for this region. 	no	yes	hifiasm misses haplotype in homopolymer due to homozygous region																											7:140504206	140804406
Common		GRCh37			7	chr7	140504206	140804406	72887	FP_FN	T	TG	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:100:i1_5:INDEL:het	CommonFP_FN			no	yes	hifiasm misses haplotype in homopolymer due to homozygous region													1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:116.73:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:98.73:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:30:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:441.64:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:0:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:50:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:16:i1_5:INDEL:het	7:140504206	140804406
Common		GRCh37			7	chr7	140577093	140877293	0	FP_FN	TGGG	T,TGGGG	GT:BD:BK:BI:QQ:BVT:BLT	2|1:FN:am:d1_5,i1_5:.:INDEL:hetalt	0/1:FP:am:d1_5:100:INDEL:het	CommonFP_FN			no	yes	Homopolymer error due to noisy HiFi reads in G homopolymer													2|1:FN:am:d1_5,i1_5:.:INDEL:hetalt	0/1:FP:am:d1_5:1155.37:INDEL:het	2|1:FN:am:d1_5,i1_5:.:INDEL:hetalt	0/1:FP:am:d1_5:1137.73:INDEL:het	2|1:FN:am:d1_5,i1_5:.:INDEL:hetalt	0/1:FP:am:d1_5:30:INDEL:het	2|1:FN:am:d1_5,i1_5:.:INDEL:hetalt	0/1:FP:am:d1_5:1112.6:INDEL:het	2|1:FN:am:d1_5,i1_5:.:INDEL:hetalt	0/1:FP:am:d1_5:0:INDEL:het	2|1:FN:am:d1_5,i1_5:.:INDEL:hetalt	0/1:FP:am:d1_5:50:INDEL:het	2|1:FN:am:d1_5,i1_5:.:INDEL:hetalt	0/1:FP:am:d1_5:10:INDEL:het	7:140577093	140877293
Common		GRCh38			7	chr7	140577093	140877293	7136	FP_FN	TGGG	T,TGGGG	GT:BD:BK:BI:QQ:BVT:BLT	2|1:FN:am:d1_5,i1_5:.:INDEL:hetalt	0/1:FP:am:d1_5:100:INDEL:het	CommonFP_FN			no	yes	Homopolymer error due to noisy HiFi reads in G homopolymer													2|1:FN:am:d1_5,i1_5:.:INDEL:hetalt	0/1:FP:am:d1_5:1155.37:INDEL:het	2|1:FN:am:d1_5,i1_5:.:INDEL:hetalt	0/1:FP:am:d1_5:1142.73:INDEL:het	2|1:FN:am:d1_5,i1_5:.:INDEL:hetalt	0/1:FP:am:d1_5:30:INDEL:het	2|1:FN:am:d1_5,i1_5:.:INDEL:hetalt	0/1:FP:am:d1_5:436.6:INDEL:het	2|1:FN:am:d1_5,i1_5:.:INDEL:hetalt	0/1:FP:am:d1_5:0:INDEL:het	2|1:FN:am:d1_5,i1_5:.:INDEL:hetalt	0/1:FP:am:d1_5:50:INDEL:het	2|1:FN:am:d1_5,i1_5:.:INDEL:hetalt	0/1:FP:am:d1_5:10:INDEL:het		140577093
CMH_DRAGEN_3.6.3	NA24385.hard-filtered.vcf.gz	GRCh37	small-variants	INDEL	7	chr7	140584229	140884429	11270423	FP_FN	A	ATGTG,ATG	GT:BD:BK:QQ:BI:BVT:BLT	2|0:FN:lm:.:i1_5:INDEL:het	0/1:FP:lm:36.48:i1_5:INDEL:het	yes	no																															7:140584229	140884429
ITER	ITERteam_small-variation_GRCh37_ILMN-PB-ONT.vcf.gz	GRCh37	small-variants	INDEL	7	chr7	151851937	152154852	24807	FP	CA	C	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	1/1:5.8:FP:.:d1_5:INDEL:homalt	Yes	No																															7:151851937	152154852
Common		GRCh38			7	chr7	151876744	152179659	56631	FP	TG	T	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:.:d1_5:INDEL:het	CommonFP			unsure	unsure	G homopolymer is noisy across techs													.:.:.:.:.:NOCALL:nocall	0/1:66.73:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:47.73:FP:.:d1_5:INDEL:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:93.64:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:.:d1_5:INDEL:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.		151876744
NYGC	HG-002-2x250-b38.recalibrated.haplotypeCalls.vcf.gz	GRCh38	small-variants	SNP	7	chr7	151933375	152236290	1304	FP_FN	A	G	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:ti:SNP:homalt	0/1:FP:am:1347.77:ti:SNP:het 	yes	no								skip																								151933375
BCM-HGSC_xAtlas	HG002.GRCh38.60x.1_merged.vcf.gz	GRCh38	small-variants	SNP	7	chr7	151934679	152237594	715	FP	T	A	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:4:FP:.:tv:SNP:het 	Yes	No								skip																								151934679
NYGC	HG-002-2x250-b38.recalibrated.haplotypeCalls.vcf.gz	GRCh38	small-variants	INDEL	7	chr7	151935394	152238309	15	FP	A	AT	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:449.73:FP:.:i1_5:INDEL:het 	yes	no								skip																								151935394
ITER	ITERteam_small-variation_GRCh38_ILMN-PB-ONT.vcf.gz	GRCh38	small-variants	SNP	7	chr7	151935409	152238324	297	FP	A	C	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:70.6:FP:.:tv:SNP:het	Yes	No	Only query short reads support the variant (plus few reads from 10X), and with low MQ.							skip																								151935409
CMH_DRAGEN_3.6.3	NA24385.hard-filtered.vcf.gz	GRCh37	small-variants	INDEL	7	chr7	151935706	152238621	0	FP	AAAAG	A	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:45.6:FP:.:d1_5:INDEL:het	unsure	unsure	In segdup/selfchain. Query looks better supported by coverage alone, but alleles aren't consistent among reads with same haplotag. Possibly with phasing error?	no	yes	hifiasm misses del in highly homozygous region																											7:151935706	152238621
Common		GRCh37			7	chr7	151935706	152238621	0	FP	AAAAG	A	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:.:d1_5:INDEL:het	CommonFP			no	yes	hifiasm misses del in highly homozygous region													.:.:.:.:.:NOCALL:nocall	0/1:814.73:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:994.73:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:22.1:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:45.6:FP:.:d1_5:INDEL:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	7:151935706	152238621
Common		GRCh38			7	chr7	151935706	152238621	1412	FP	AAAAG	A	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:.:d1_5:INDEL:het	CommonFP			no	yes	hifiasm misses del in highly homozygous region													.:.:.:.:.:NOCALL:nocall	0/1:814.73:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:1000.73:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:718.6:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:45.6:FP:.:d1_5:INDEL:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.		151935706
BCM-HGSC_xAtlas	HG002.hs37d5.60x.1_merged.vcf.gz	GRCh37	small-variants	SNP	7	chr7	151937118	152240033	4680	FP	A	G	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:34:FP:.:ti:SNP:het 	Yes	No																															7:151937118	152240033
BCM-HGSC_xAtlas	HG002.hs37d5.60x.1_merged.vcf.gz	GRCh37	small-variants	SNP	7	chr7	151941798	152244713	263	FP	G	A	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:26:FP:.:ti:SNP:het 	Yes	No																															7:151941798	152244713
CMH_DRAGEN_3.6.3	NA24385.hard-filtered.vcf.gz	GRCh37	small-variants	SNP	7	chr7	151942061	152244976	47	FP	G	C	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:40.51:FP:.:tv:SNP:het	yes	no																															7:151942061	152244976
CMH_DRAGEN_3.6.3	NA24385.hard-filtered.vcf.gz	GRCh37	small-variants	SNP	7	chr7	151942108	152245023	2408	FP	C	T	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:37.43:FP:.:ti:SNP:het	yes	no																															7:151942108	152245023
CMH_DRAGEN_3.6.3	NA24385.hard-filtered.vcf.gz	GRCh37	small-variants	SNP	7	chr7	151944516	152247431	186	FP	T	C	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:38.36:FP:.:ti:SNP:het	yes	no	In segdup/selfchain. Short reads only and surrounding region covered unevenly																														7:151944516	152247431
Common		GRCh38			7	chr7	151944702	152247617	13395	FP_FN	A	G	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:27.2143:ti:SNP:homalt	1/1:TP:gm:27.2143:ti:SNP:homalt	CommonFP_FN			yes	no	error in short reads due to mismapped reads in KMT2C													1|1:TP:gm:1988.77:ti:SNP:homalt	1/1:TP:gm:1988.77:ti:SNP:homalt	1|1:FN:am:.:ti:SNP:homalt	0/1:FP:am:1019.77:ti:SNP:het	1|1:FN:am:.:ti:SNP:homalt	0/1:FP:am:30:ti:SNP:het	1|1:FN:am:.:ti:SNP:homalt	0/1:FP:am:1186.6:ti:SNP:het	1|1:FN:am:.:ti:SNP:homalt	0/1:FP:am:0:ti:SNP:het	1|1:TP:gm:51.21:ti:SNP:homalt	1/1:TP:gm:51.21:ti:SNP:homalt	1|1:FN:am:.:ti:SNP:homalt	0/1:FP:am:39:ti:SNP:het		151944702
CMH_DRAGEN_3.6.3	NA24385.hard-filtered.vcf.gz	GRCh37	small-variants	INDEL	7	chr7	151958097	152261012	14	FP	AG	A	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:34.14:FP:.:d1_5:INDEL:het	yes	no																															7:151958097	152261012
CMH_DRAGEN_3.6.3	NA24385.hard-filtered.vcf.gz	GRCh38	small-variants	SNP	7	chr7	151958111	152261026	8256	FP	C	A	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:35.72:FP:.:tv:SNP:het	yes	no								skip																								151958111
NCBI	HG002_grch37_dipcall.vcf.gz	GRCh37	small-variants	INDEL	7	chr7	151966367	152269282	3058	FP	AATAC	A	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:.:d1_5:INDEL:het	yes	no	segdup; only ONT for query																														7:151966367	152269282
NCBI	HG002_grch37_dipcall.vcf.gz	GRCh37	small-variants	SNP	7	chr7	151969425	152272340	3880	FP	C	T	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	1/1:30:FP:.:ti:SNP:homalt	yes	no	segdup region																														7:151969425	152272340
NCBI	HG002_grch38_dipcall.vcf.gz	GRCh38	small-variants	SNP	7	chr7	151973305	152276220	2023	FP	T	C	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:.:ti:SNP:het	yes	no	segdup region							skip																								151973305
NCBI	HG002_grch37_dipcall.vcf.gz	GRCh37	small-variants	SNP	7	chr7	151975328	152278243	33	FP	C	T	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	1/1:30:FP:.:ti:SNP:homalt	yes	no	segdup region																														7:151975328	152278243
NCBI	HG002_grch37_dipcall.vcf.gz	GRCh37	small-variants	INDEL	7	chr7	151975361	152278276	566	FP	T	TTAAA	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:.:i1_5:INDEL:het	yes	no	segdup region																														7:151975361	152278276
Common		GRCh37			7	chr7	151975927	152278842	1144	FP	A	G	GT:QQ:BD:BK:BI:BVT:BLT	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	CommonFP			yes	no	FP in short reads due to mismapped reads in dup in KMT2C													./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:1971.77:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	1/1:30:FP:.:ti:SNP:homalt	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:30.74:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:26:FP:.:ti:SNP:het	7:151975927	152278842
BCM-HGSC_xAtlas	HG002.hs37d5.60x.1_merged.vcf.gz	GRCh37	small-variants	SNP	7	chr7	151977071	152279986	18911	FP	T	C	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:21:FP:.:ti:SNP:het 	Yes	No																															7:151977071	152279986
PacBio_gatk4	gatk4hc_HG002_15kb_20kb_52X_SequelII.vcf.gz	GRCh37	small-variants	INDEL	7	chr7	151995982	152298897	0	FN	TTATA	T	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	no	yes	no read support	no	yes	hifiasm misses these nearby del and ins on opposite haplotypes for unclear reasons																											7:151995982	152298897
Common		GRCh37			7	chr7	151995982	152298897	0	FN	TTATA	T	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no	yes	hifiasm misses these nearby del and ins on opposite haplotypes for unclear reasons													0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	7:151995982	152298897
Common		GRCh38			7	chr7	151995982	152298897	422	FN	TTATA	T	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no	yes	hifiasm misses these nearby del and ins on opposite haplotypes for unclear reasons													0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0		151995982
Common		GRCh37			7	chr7	151996404	152299319	0	FP	A	AAAAT	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:.:i1_5:INDEL:het	CommonFP			no	yes	hifiasm misses these nearby del and ins on opposite haplotypes for unclear reasons													.:.:.:.:.:NOCALL:nocall	0/1:421.73:FP:.:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:451.73:FP:.:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:.:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:493.64:FP:.:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:.:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:43.93:FP:.:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:9:FP:.:i1_5:INDEL:het	7:151996404	152299319
Common		GRCh38			7	chr7	151996404	152299319	60754	FP	A	AAAAT	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:.:i1_5:INDEL:het	CommonFP			no	yes	hifiasm misses these nearby del and ins on opposite haplotypes for unclear reasons													.:.:.:.:.:NOCALL:nocall	0/1:421.73:FP:.:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:412.73:FP:.:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:.:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:204.64:FP:.:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:.:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:43.95:FP:.:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:9:FP:.:i1_5:INDEL:het		151996404
Common		GRCh37			7	chr7	152057158	152360073	0	FP	TG	T	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:lm:d1_5:INDEL:het	CommonFP			unsure	unsure	G homopolymer is noisy across techs													./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:46.73:FP:lm:d1_5:INDEL:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:76.6:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:50.01:FP:lm:d1_5:INDEL:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	7:152057158	152360073
Common		GRCh38			7	chr7	152057158	152360073	4861	FP	TG	T	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:lm:d1_5:INDEL:het	CommonFP			unsure	unsure	G homopolymer is noisy across techs													./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:46.73:FP:lm:d1_5:INDEL:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:22.63:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:50.01:FP:lm:d1_5:INDEL:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.		152057158
Common		GRCh37			7	chr7	152062019	152364934	0	FP	GAC	G	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:lm:d1_5:INDEL:het	CommonFP			no	yes	hifiasm miscalls hom insertion likely due to highly homozygous region and noisy TR													.:.:.:.:.:NOCALL:nocall	0/1:598.73:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:1247.73:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:770.06:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:am:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:181.15:FP:lm:d1_5:INDEL:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	7:152062019	152364934
ITER	ITERteam_small-variation_GRCh38_ILMN-PB-ONT.vcf.gz	GRCh38	small-variants	INDEL	7	chr7	152062019	152364934	0	FP	GAC	G	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:420.06:FP:lm:d1_5:INDEL:het	No	Yes	We both called a 2nt insertion but in a different manner (truth as G:GAC and query as GAC:GACAC). But, truth did not call this deletion (GAC:G) that is well supported by all technologies in truth and query.	no	yes	hifiasm miscalls hom insertion likely due to highly homozygous region and noisy TR																												152062019
Common		GRCh38			7	chr7	152062019	152364934	2	FP	GAC	G	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:lm:d1_5:INDEL:het	CommonFP			no	yes	hifiasm miscalls hom insertion likely due to highly homozygous region and noisy TR													.:.:.:.:.:NOCALL:nocall	0/1:598.73:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:1247.73:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:420.06:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:am:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:182.25:FP:lm:d1_5:INDEL:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.		152062019
Common		GRCh37			7	chr7	152062021	152364936	0	FP	C	CAC	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:am:i1_5:INDEL:het	CommonFP			no	yes	hifiasm miscalls hom insertion likely due to highly homozygous region and noisy TR													.:.:.:.:.:NOCALL:nocall	0/1:598.73:FP:am:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:1247.73:FP:am:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:am:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:770.06:FP:am:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:am:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:181.15:FP:am:i1_5:INDEL:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	7:152062021	152364936
Common		GRCh38			7	chr7	152062021	152364936	15168	FP	C	CAC	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:am:i1_5:INDEL:het	CommonFP			no	yes	hifiasm miscalls hom insertion likely due to highly homozygous region and noisy TR													.:.:.:.:.:NOCALL:nocall	0/1:598.73:FP:am:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:1247.73:FP:am:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:am:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:420.06:FP:am:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:am:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:182.25:FP:am:i1_5:INDEL:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.		152062021
CMH_DRAGEN_3.6.3	NA24385.hard-filtered.vcf.gz	GRCh38	small-variants	SNP	7	chr7	152077189	152380104	3081	FP	T	C	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:33.19:FP:.:ti:SNP:het	yes	no								skip																								152077189
BCM-HGSC_xAtlas	HG002.GRCh38.60x.1_merged.vcf.gz	GRCh38	small-variants	INDEL	7	chr7	152080270	152383185	1531	FP	C	CT	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:18:FP:.:i1_5:INDEL:het 	Yes	No								skip																								152080270
BCM-HGSC_xAtlas	HG002.GRCh38.60x.1_merged.vcf.gz	GRCh38	small-variants	SNP	7	chr7	152081801	152384716	2753	FP	A	G	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:27:FP:.:ti:SNP:het 	Yes	No								skip																								152081801
Common		GRCh37			7	chr7	152084554	152387469	0	FN	A	AT	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			unsure	unsure	probably hifiasm error due to noisy long homopolymer but in seg dup and 10x has high coverage so short read mapping may be suspect													1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	7:152084554	152387469
Common		GRCh38			7	chr7	152084554	152387469	1104	FN	A	AT	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			unsure	unsure	probably hifiasm error due to noisy long homopolymer but in seg dup and 10x has high coverage so short read mapping may be suspect													1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0		152084554
BCM-HGSC_xAtlas	HG002.GRCh38.60x.1_merged.vcf.gz	GRCh38	small-variants	SNP	7	chr7	152085658	152388573	12582	FP	C	T	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:13:FP:.:ti:SNP:het 	Yes	No								skip																								152085658
ITER	ITERteam_small-variation_GRCh38_ILMN-PB-ONT.vcf.gz	GRCh38	small-variants	SNP	7	chr7	152098240	152401155	193	FP	G	T	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:17.7:FP:.:tv:SNP:het	Unsure	Unsure	There is no evidence of variant in short reads. Long reads do support this variant, with high depth and MQ.	yes	no	in region of many FPs due to mismapped reads from extra regions in HG002 that are missing in GRCh38 so are mismapped to KMT2C																												152098240
ITER	ITERteam_small-variation_GRCh38_ILMN-PB-ONT.vcf.gz	GRCh38	small-variants	SNP	7	chr7	152098433	152401348	484	FP	G	A	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:4.2:FP:.:ti:SNP:het	Unsure	Unsure	There is no evidence of variant in short reads. Long reads do support this variant, with high depth and MQ.	yes	no	in region of many FPs due to mismapped reads from extra regions in HG002 that are missing in GRCh38 so are mismapped to KMT2C																												152098433
Common		GRCh38			7	chr7	152098917	152401832	100	FP	C	T	GT:QQ:BD:BK:BI:BVT:BLT	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	CommonFP			yes	no	in region of many FPs due to mismapped reads from extra regions in HG002 that are missing in GRCh38 so are mismapped to KMT2C													.:.:.:.:.:NOCALL:nocall	0/1:2723.77:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:1534.77:FP:.:ti:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:24.5:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:.:ti:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:.:ti:SNP:het		152098917
Common		GRCh38			7	chr7	152099017	152401932	185	FP	G	A	GT:QQ:BD:BK:BI:BVT:BLT	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	CommonFP			yes	no	in region of many FPs due to mismapped reads from extra regions in HG002 that are missing in GRCh38 so are mismapped to KMT2C													.:.:.:.:.:NOCALL:nocall	0/1:2398.77:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:1186.77:FP:.:ti:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:22.2:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:.:ti:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:14:FP:.:ti:SNP:het		152099017
NYGC	HG-002-2x250-b37.recalibrated.haplotypeCalls.vcf.gz	GRCh37	small-variants	INDEL	7	chr7	152099202	152402117	318	FP	AC	A	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:3484.73:FP:.:d1_5:INDEL:het 	yes	no	some evidence of a larger deletion in the 10X but i think this is an alignment issue since no evidence in PacBio																														7:152099202	152402117
Common		GRCh38			7	chr7	152099520	152402435	55	FP	C	A	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:31.5498:FP:.:tv:SNP:het	CommonFP			yes	no	in region of many FPs due to mismapped reads from extra regions in HG002 that are missing in GRCh38 so are mismapped to KMT2C													.:.:.:.:.:NOCALL:nocall	0/1:2883.77:FP:.:tv:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:9531.77:FP:.:tv:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:140.6:FP:.:tv:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:14:FP:.:tv:SNP:het		152099520
Roche	RN_HG002_Illumina_PacBio_Oxford.vcf.gz	GRCh38	small-variants	SNP	7	chr7	152099575	152402490	0	FP	C	T	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:22.6817:FP:.:ti:SNP:het 	no	yes	the variant seems clear from ILM/PB/ONT, not sure why it is not in the assembly (also the neighboring variant at chr7-152402501-A-C)	yes	no	in region of many FPs due to mismapped reads from extra regions in HG002 that are missing in GRCh38 so are mismapped to KMT2C																												152099575
Common		GRCh38			7	chr7	152099575	152402490	45	FP	C	T	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:22.6817:FP:.:ti:SNP:het	CommonFP			yes	no	in region of many FPs due to mismapped reads from extra regions in HG002 that are missing in GRCh38 so are mismapped to KMT2C													.:.:.:.:.:NOCALL:nocall	0/1:2925.77:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:9070.77:FP:.:ti:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:117.6:FP:.:ti:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:17:FP:.:ti:SNP:het		152099575
Common		GRCh38			7	chr7	152099620	152402535	286	FP	T	G	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:16.0615:FP:.:tv:SNP:het	CommonFP			yes	no	in region of many FPs due to mismapped reads from extra regions in HG002 that are missing in GRCh38 so are mismapped to KMT2C													.:.:.:.:.:NOCALL:nocall	0/1:1687.77:FP:.:tv:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:7095.77:FP:.:tv:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:81.6:FP:.:tv:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:7:FP:.:tv:SNP:het		152099620
Common		GRCh38			7	chr7	152099906	152402821	11	FP	T	A	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:.:tv:SNP:het	CommonFP			yes	no	in region of many FPs due to mismapped reads from extra regions in HG002 that are missing in GRCh38 so are mismapped to KMT2C													.:.:.:.:.:NOCALL:nocall	0/1:2241.77:FP:.:tv:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:10402.8:FP:.:tv:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:11.7:FP:.:tv:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:36:FP:.:tv:SNP:het		152099906
Common		GRCh38			7	chr7	152099917	152402832	7	FP	G	A	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:.:ti:SNP:het	CommonFP			yes	no	in region of many FPs due to mismapped reads from extra regions in HG002 that are missing in GRCh38 so are mismapped to KMT2C													.:.:.:.:.:NOCALL:nocall	0/1:2286.77:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:10630.8:FP:.:ti:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:23.2:FP:.:ti:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:20.65:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:39:FP:.:ti:SNP:het		152099917
Common		GRCh38			7	chr7	152099924	152402839	65	FP	T	C	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:.:ti:SNP:het	CommonFP			yes	no	in region of many FPs due to mismapped reads from extra regions in HG002 that are missing in GRCh38 so are mismapped to KMT2C													.:.:.:.:.:NOCALL:nocall	0/1:2286.77:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:10096.8:FP:.:ti:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:10.7:FP:.:ti:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:23.29:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:37:FP:.:ti:SNP:het		152099924
Common		GRCh38			7	chr7	152099989	152402904	64	FP	T	A	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:32.2186:FP:.:tv:SNP:het	CommonFP			yes	no	in region of many FPs due to mismapped reads from extra regions in HG002 that are missing in GRCh38 so are mismapped to KMT2C													.:.:.:.:.:NOCALL:nocall	0/1:2301.77:FP:.:tv:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:7190.77:FP:.:tv:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:17.7:FP:.:tv:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:.:tv:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:50.04:FP:.:tv:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:26:FP:.:tv:SNP:het		152099989
Common		GRCh38			7	chr7	152100053	152402968	138	FP	GACAT	G	GT:QQ:BD:BK:BI:BVT:BLT	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	CommonFP			yes	no	in region of many FPs due to mismapped reads from extra regions in HG002 that are missing in GRCh38 so are mismapped to KMT2C													.:.:.:.:.:NOCALL:nocall	0/1:2361.73:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:7551.73:FP:.:d1_5:INDEL:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:18.8:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	1/1:79.22:FP:.:d1_5:INDEL:homalt	.:.:.:.:.:NOCALL:nocall	1/1:15:FP:.:d1_5:INDEL:homalt		152100053
Common		GRCh38			7	chr7	152100191	152403106	1	FP	T	C	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:.:ti:SNP:het	CommonFP			yes	no	in region of many FPs due to mismapped reads from extra regions in HG002 that are missing in GRCh38 so are mismapped to KMT2C													.:.:.:.:.:NOCALL:nocall	0/1:3270.77:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:10958.8:FP:.:ti:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:13.5:FP:.:ti:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	1/1:189.86:FP:.:ti:SNP:homalt	.:.:.:.:.:NOCALL:nocall	0/1:29:FP:.:ti:SNP:het		152100191
ITER	ITERteam_small-variation_GRCh38_ILMN-PB-ONT.vcf.gz	GRCh38	small-variants	SNP	7	chr7	152100192	152403107	0	FP	G	A	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:7.6:FP:.:ti:SNP:het	No	Yes	All technologies support this variant. The variant in previous position is also supported by all technologies (not called in truth either).	yes	no	in region of many FPs due to mismapped reads from extra regions in HG002 that are missing in GRCh38 so are mismapped to KMT2C																												152100192
Common		GRCh38			7	chr7	152100192	152403107	21	FP	G	A	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:5.5037:FP:.:ti:SNP:het	CommonFP			yes	no	in region of many FPs due to mismapped reads from extra regions in HG002 that are missing in GRCh38 so are mismapped to KMT2C													.:.:.:.:.:NOCALL:nocall	0/1:3270.77:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:11081.8:FP:.:ti:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:7.6:FP:.:ti:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	1/1:190.23:FP:.:ti:SNP:homalt	.:.:.:.:.:NOCALL:nocall	0/1:29:FP:.:ti:SNP:het		152100192
Common		GRCh38			7	chr7	152100213	152403128	7	FP	G	A	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:22.5197:FP:.:ti:SNP:het	CommonFP			yes	no	in region of many FPs due to mismapped reads from extra regions in HG002 that are missing in GRCh38 so are mismapped to KMT2C													.:.:.:.:.:NOCALL:nocall	0/1:3268.77:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:11483.8:FP:.:ti:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:22.3:FP:.:ti:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	1/1:206.13:FP:.:ti:SNP:homalt	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:.:ti:SNP:het		152100213
NYGC	HG-002-2x250-b37.recalibrated.haplotypeCalls.vcf.gz	GRCh37	small-variants	INDEL	7	chr7	152100220	152403135	3	FP	AC	A	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:1093.73:FP:.:d1_5:INDEL:het 	yes	no																															7:152100220	152403135
CMH_DRAGEN_3.6.3	NA24385.hard-filtered.vcf.gz	GRCh38	small-variants	INDEL	7	chr7	152100223	152403138	0	FP	TA	T	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	1/1:59.17:FP:.:d1_5:INDEL:homalt	unsure	unsure	Multiple conflicting evidences exist. In a series of repeat elements. Not sure how to make sense of it or which is more probable	yes	no	in region of many FPs due to mismapped reads from extra regions in HG002 that are missing in GRCh38 so are mismapped to KMT2C																												152100223
Common		GRCh38			7	chr7	152100223	152403138	32	FP	TA	T	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:29.5865:FP:.:d1_5:INDEL:het	CommonFP			yes	no	in region of many FPs due to mismapped reads from extra regions in HG002 that are missing in GRCh38 so are mismapped to KMT2C													.:.:.:.:.:NOCALL:nocall	0/1:2087.73:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:8792.73:FP:.:d1_5:INDEL:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:18:FP:.:d1_5:INDEL:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	1/1:59.17:FP:.:d1_5:INDEL:homalt	.:.:.:.:.:NOCALL:nocall	0/1:10:FP:.:d1_5:INDEL:het		152100223
PacBio_gatk4	gatk4hc_HG002_15kb_20kb_53X_SequelII.vcf.gz	GRCh38	small-variants	SNP	7	chr7	152100255	152403170	0	FP	C	T	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:3233.77:FP:.:ti:SNP:het	yes	no		yes	no	in region of many FPs due to mismapped reads from extra regions in HG002 that are missing in GRCh38 so are mismapped to KMT2C				skip																								152100255
Common		GRCh38			7	chr7	152100255	152403170	54	FP	C	T	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:.:ti:SNP:het	CommonFP			yes	no	in region of many FPs due to mismapped reads from extra regions in HG002 that are missing in GRCh38 so are mismapped to KMT2C													.:.:.:.:.:NOCALL:nocall	0/1:3233.77:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:8898.77:FP:.:ti:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:4.8:FP:.:ti:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	1/1:214.45:FP:.:ti:SNP:homalt	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:.:ti:SNP:het		152100255
Common		GRCh38			7	chr7	152100309	152403224	4	FP	G	A	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:.:ti:SNP:het	CommonFP			yes	no	in region of many FPs due to mismapped reads from extra regions in HG002 that are missing in GRCh38 so are mismapped to KMT2C													.:.:.:.:.:NOCALL:nocall	0/1:1440.77:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:8756.77:FP:.:ti:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:11.9:FP:.:ti:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	1/1:231.96:FP:.:ti:SNP:homalt	.:.:.:.:.:NOCALL:nocall	0/1:26:FP:.:ti:SNP:het		152100309
Common		GRCh38			7	chr7	152100313	152403228	3	FP	G	A	GT:QQ:BD:BK:BI:BVT:BLT	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	CommonFP			yes	no	in region of many FPs due to mismapped reads from extra regions in HG002 that are missing in GRCh38 so are mismapped to KMT2C													.:.:.:.:.:NOCALL:nocall	0/1:540.77:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:5572.77:FP:.:ti:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:9.6:FP:.:ti:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:49.9:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:33:FP:.:ti:SNP:het		152100313
Common		GRCh38			7	chr7	152100316	152403231	10	FP	A	G	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:30.97:FP:.:ti:SNP:het	CommonFP			yes	no	in region of many FPs due to mismapped reads from extra regions in HG002 that are missing in GRCh38 so are mismapped to KMT2C													.:.:.:.:.:NOCALL:nocall	0/1:1440.77:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:7489.77:FP:.:ti:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:10.5:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	1/1:118.71:FP:.:ti:SNP:homalt	.:.:.:.:.:NOCALL:nocall	0/1:23:FP:.:ti:SNP:het		152100316
PacBio_gatk4	gatk4hc_HG002_15kb_20kb_53X_SequelII.vcf.gz	GRCh38	small-variants	SNP	7	chr7	152100326	152403241	0	FP	G	A	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:1440.77:FP:.:ti:SNP:het	yes	no		yes	no	in region of many FPs due to mismapped reads from extra regions in HG002 that are missing in GRCh38 so are mismapped to KMT2C				skip																								152100326
Common		GRCh38			7	chr7	152100326	152403241	44	FP	G	A	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:.:ti:SNP:het	CommonFP			yes	no	in region of many FPs due to mismapped reads from extra regions in HG002 that are missing in GRCh38 so are mismapped to KMT2C													.:.:.:.:.:NOCALL:nocall	0/1:1440.77:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:8569.77:FP:.:ti:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:24.6:FP:.:ti:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	1/1:263.7:FP:.:ti:SNP:homalt	.:.:.:.:.:NOCALL:nocall	0/1:27:FP:.:ti:SNP:het		152100326
Common		GRCh38			7	chr7	152100370	152403285	51	FP	C	G	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:.:tv:SNP:het	CommonFP			yes	no	in region of many FPs due to mismapped reads from extra regions in HG002 that are missing in GRCh38 so are mismapped to KMT2C													.:.:.:.:.:NOCALL:nocall	0/1:1397.77:FP:.:tv:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:6767.77:FP:.:tv:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:14.8:FP:.:tv:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	1/1:202.36:FP:.:tv:SNP:homalt	.:.:.:.:.:NOCALL:nocall	0/1:25:FP:.:tv:SNP:het		152100370
Common		GRCh38			7	chr7	152100421	152403336	34	FP	C	T	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:.:ti:SNP:het	CommonFP			yes	no	in region of many FPs due to mismapped reads from extra regions in HG002 that are missing in GRCh38 so are mismapped to KMT2C													.:.:.:.:.:NOCALL:nocall	0/1:1438.77:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:6588.77:FP:.:ti:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:16.6:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	1/1:216.6:FP:.:ti:SNP:homalt	.:.:.:.:.:NOCALL:nocall	0/1:28:FP:.:ti:SNP:het		152100421
Common		GRCh38			7	chr7	152100455	152403370	5	FP	G	A	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:.:ti:SNP:het	CommonFP			yes	no	in region of many FPs due to mismapped reads from extra regions in HG002 that are missing in GRCh38 so are mismapped to KMT2C													.:.:.:.:.:NOCALL:nocall	0/1:1443.77:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:8227.77:FP:.:ti:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:9.3:FP:.:ti:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	1/1:244.12:FP:.:ti:SNP:homalt	.:.:.:.:.:NOCALL:nocall	0/1:37:FP:.:ti:SNP:het		152100455
Common		GRCh38			7	chr7	152100460	152403375	5	FP	G	GCC,GCCAT	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:28.2391:FP:.:i1_5:INDEL:het	CommonFP			yes	no	in region of many FPs due to mismapped reads from extra regions in HG002 that are missing in GRCh38 so are mismapped to KMT2C													.:.:.:.:.:NOCALL:nocall	0/1:1434.73:FP:.:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:8466.73:FP:.:i1_5:INDEL:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	1/1:250.15:FP:.:i1_5:INDEL:homalt	.:.:.:.:.:NOCALL:nocall	0/2:17:FP:.:i1_5:INDEL:het		152100460
Common		GRCh38			7	chr7	152100465	152403380	21	FP	GCA	G	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:28.2391:FP:.:d1_5:INDEL:het	CommonFP			yes	no	in region of many FPs due to mismapped reads from extra regions in HG002 that are missing in GRCh38 so are mismapped to KMT2C													.:.:.:.:.:NOCALL:nocall	0/1:1434.73:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:8356.73:FP:.:d1_5:INDEL:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:6.3:FP:.:d1_5:INDEL:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	1/1:277.88:FP:.:d1_5:INDEL:homalt	.:.:.:.:.:NOCALL:nocall	0/1:2:FP:.:d1_5:INDEL:het		152100465
Common		GRCh38			7	chr7	152100486	152403401	59	FP	C	T	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:.:ti:SNP:het	CommonFP			yes	no	in region of many FPs due to mismapped reads from extra regions in HG002 that are missing in GRCh38 so are mismapped to KMT2C													.:.:.:.:.:NOCALL:nocall	0/1:1446.77:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:8743.77:FP:.:ti:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:11.6:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	1/1:289.1:FP:.:ti:SNP:homalt	.:.:.:.:.:NOCALL:nocall	0/1:32:FP:.:ti:SNP:het		152100486
Common		GRCh38			7	chr7	152100545	152403460	30	FP	T	C	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:.:ti:SNP:het	CommonFP			yes	no	in region of many FPs due to mismapped reads from extra regions in HG002 that are missing in GRCh38 so are mismapped to KMT2C													.:.:.:.:.:NOCALL:nocall	0/1:2862.77:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:8295.77:FP:.:ti:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:10.6:FP:.:ti:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	1/1:267.28:FP:.:ti:SNP:homalt	.:.:.:.:.:NOCALL:nocall	0/1:24:FP:.:ti:SNP:het		152100545
Common		GRCh38			7	chr7	152100575	152403490	16	FP	C	A	GT:QQ:BD:BK:BI:BVT:BLT	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	CommonFP			yes	no	in region of many FPs due to mismapped reads from extra regions in HG002 that are missing in GRCh38 so are mismapped to KMT2C													.:.:.:.:.:NOCALL:nocall	0/1:1329.77:FP:.:tv:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:5819.77:FP:.:tv:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:.:tv:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:50:FP:.:tv:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:35:FP:.:tv:SNP:het		152100575
Common		GRCh38			7	chr7	152100591	152403506	3	FP	T	A	GT:QQ:BD:BK:BI:BVT:BLT	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	CommonFP			yes	no	in region of many FPs due to mismapped reads from extra regions in HG002 that are missing in GRCh38 so are mismapped to KMT2C													.:.:.:.:.:NOCALL:nocall	0/1:1326.77:FP:.:tv:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:5692.77:FP:.:tv:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:.:tv:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:50:FP:.:tv:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:35:FP:.:tv:SNP:het		152100591
Common		GRCh38			7	chr7	152100594	152403509	166	FP	C	G	GT:QQ:BD:BK:BI:BVT:BLT	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	CommonFP			yes	no	in region of many FPs due to mismapped reads from extra regions in HG002 that are missing in GRCh38 so are mismapped to KMT2C													.:.:.:.:.:NOCALL:nocall	0/1:2901.77:FP:.:tv:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:8539.77:FP:.:tv:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:11.5:FP:.:tv:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	1/1:200.95:FP:.:tv:SNP:homalt	.:.:.:.:.:NOCALL:nocall	0/1:25:FP:.:tv:SNP:het		152100594
Common		GRCh38			7	chr7	152100760	152403675	12	FP	T	C	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:.:ti:SNP:het	CommonFP			yes	no	in region of many FPs due to mismapped reads from extra regions in HG002 that are missing in GRCh38 so are mismapped to KMT2C													.:.:.:.:.:NOCALL:nocall	0/1:2787.77:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:6055.77:FP:.:ti:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:28:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	1/1:190.46:FP:.:ti:SNP:homalt	.:.:.:.:.:NOCALL:nocall	0/1:29:FP:.:ti:SNP:het		152100760
Common		GRCh38			7	chr7	152100772	152403687	18	FP	C	T	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:.:ti:SNP:het	CommonFP			yes	no	in region of many FPs due to mismapped reads from extra regions in HG002 that are missing in GRCh38 so are mismapped to KMT2C													.:.:.:.:.:NOCALL:nocall	0/1:2787.77:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:6031.77:FP:.:ti:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:34.1:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	1/1:171.25:FP:.:ti:SNP:homalt	.:.:.:.:.:NOCALL:nocall	0/1:27:FP:.:ti:SNP:het		152100772
Common		GRCh38			7	chr7	152100790	152403705	10	FP	C	T	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:.:ti:SNP:het	CommonFP			yes	no	in region of many FPs due to mismapped reads from extra regions in HG002 that are missing in GRCh38 so are mismapped to KMT2C													.:.:.:.:.:NOCALL:nocall	0/1:2787.77:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:5701.77:FP:.:ti:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:39.1:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	1/1:148.41:FP:.:ti:SNP:homalt	.:.:.:.:.:NOCALL:nocall	0/1:23:FP:.:ti:SNP:het		152100790
Common		GRCh37			7	chr7	152100800	152403715	0	FP	TAC	TACAC,T	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/2:100:FP:.:d1_5:INDEL:het	CommonFP			yes	no	in region of many FPs due to mismapped reads from extra regions in HG002 that are missing in GRCh38 so are mismapped to KMT2C													.:.:.:.:.:NOCALL:nocall	0/2:330.73:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/2:1576.73:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/2:30:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/2:394.06:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/2:0:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/2:110.58:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:13:FP:.:i1_5:INDEL:het	7:152100800	152403715
NCBI	HG002_grch38_dipcall.vcf.gz	GRCh38	small-variants	INDEL	7	chr7	152100800	152403715	2	FP	TAC	T	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:.:d1_5:INDEL:het	no	unsure	2-4bps DEL for query here supported by all evidence	yes	no	in region of many FPs due to mismapped reads from extra regions in HG002 that are missing in GRCh38 so are mismapped to KMT2C																												152100800
Common		GRCh37			7	chr7	152100802	152403717	93	FP	C	CAC	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:.:i1_5:INDEL:het	CommonFP			yes	no	in region of many FPs due to mismapped reads from extra regions in HG002 that are missing in GRCh38 so are mismapped to KMT2C													.:.:.:.:.:NOCALL:nocall	0/1:330.73:FP:.:i1_5:INDEL:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:.:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:394.06:FP:.:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:.:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:110.58:FP:.:i1_5:INDEL:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	7:152100802	152403717
Common		GRCh38			7	chr7	152100895	152403810	10	FP	CGTGGAAGGATGG	CATGG,C	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:14.789:FP:.:d6_15:INDEL:het	CommonFP			yes	no	in region of many FPs due to mismapped reads from extra regions in HG002 that are missing in GRCh38 so are mismapped to KMT2C													.:.:.:.:.:NOCALL:nocall	0/1:2862.73:FP:.:d6_15:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:4957.73:FP:.:d6_15:INDEL:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:10.5:FP:.:d6_15:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:.:d6_15:INDEL:het	.:.:.:.:.:NOCALL:nocall	1/1:131.03:FP:.:d6_15:INDEL:homalt	.:.:.:.:.:NOCALL:nocall	0/2:11:FP:.:d6_15:INDEL:het		152100895
NYGC	HG-002-2x250-b38.recalibrated.haplotypeCalls.vcf.gz	GRCh38	small-variants	INDEL	7	chr7	152100905	152403820	0	FP	TGGAA	T	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:4883.73:FP:.:d1_5:INDEL:het 	no	yes	This looks like a real deletion (single larger complex indel with neighboring 8bp del) with evidence in multiple techs	yes	no	in region of many FPs due to mismapped reads from extra regions in HG002 that are missing in GRCh38 so are mismapped to KMT2C																												152100905
Common		GRCh38			7	chr7	152100905	152403820	118	FP	TGGAA	T	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:14.789:FP:.:d1_5:INDEL:het	CommonFP			yes	no	in region of many FPs due to mismapped reads from extra regions in HG002 that are missing in GRCh38 so are mismapped to KMT2C													.:.:.:.:.:NOCALL:nocall	0/1:2862.73:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:4883.73:FP:.:d1_5:INDEL:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:9.2:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	1/1:112.15:FP:.:d1_5:INDEL:homalt	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.		152100905
Common		GRCh38			7	chr7	152101023	152403938	115	FP	G	C	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:17.9762:FP:.:tv:SNP:het	CommonFP			yes	no	in region of many FPs due to mismapped reads from extra regions in HG002 that are missing in GRCh38 so are mismapped to KMT2C													.:.:.:.:.:NOCALL:nocall	0/1:2187.77:FP:.:tv:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:3045.77:FP:.:tv:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:18.9:FP:.:tv:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:.:tv:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:50:FP:.:tv:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:26:FP:.:tv:SNP:het		152101023
Common		GRCh38			7	chr7	152101138	152404053	40	FP	A	G	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:.:ti:SNP:het	CommonFP			yes	no	in region of many FPs due to mismapped reads from extra regions in HG002 that are missing in GRCh38 so are mismapped to KMT2C													.:.:.:.:.:NOCALL:nocall	0/1:3880.77:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:6461.77:FP:.:ti:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:29.8:FP:.:ti:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:26.04:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:28:FP:.:ti:SNP:het		152101138
Roche	RN_HG002_Illumina_PacBio_Oxford.vcf.gz	GRCh38	small-variants	SNP	7	chr7	152101178	152404093	0	FP	A	C	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:.:tv:SNP:het 	no	yes	the variant seems clear from all technologies, not sure why it is not in the assembly	yes	no	in region of many FPs due to mismapped reads from extra regions in HG002 that are missing in GRCh38 so are mismapped to KMT2C																												152101178
Common		GRCh38			7	chr7	152101178	152404093	68	FP	A	C	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:.:tv:SNP:het	CommonFP			yes	no	in region of many FPs due to mismapped reads from extra regions in HG002 that are missing in GRCh38 so are mismapped to KMT2C													.:.:.:.:.:NOCALL:nocall	0/1:3832.77:FP:.:tv:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:7163.77:FP:.:tv:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:10.4:FP:.:tv:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:31:FP:.:tv:SNP:het		152101178
Common		GRCh38			7	chr7	152101246	152404161	101	FP	T	C	GT:QQ:BD:BK:BI:BVT:BLT	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	CommonFP			yes	no	in region of many FPs due to mismapped reads from extra regions in HG002 that are missing in GRCh38 so are mismapped to KMT2C													.:.:.:.:.:NOCALL:nocall	0/1:798.77:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:3852.77:FP:.:ti:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:5.5:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	1/1:0:FP:.:ti:SNP:homalt	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:7:FP:.:ti:SNP:het		152101246
NYGC	HG-002-2x250-b38.recalibrated.haplotypeCalls.vcf.gz	GRCh38	small-variants	SNP	7	chr7	152101347	152404262	35	FP	T	C	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:196.77:FP:.:ti:SNP:het 	unsure	unsure	The variant is missing from the HiFi Asm, but PacBio and ONT seem to support it, although the region has high rate of polymorphism.	yes	no	in region of many FPs due to mismapped reads from extra regions in HG002 that are missing in GRCh38 so are mismapped to KMT2C																												152101347
NYGC	HG-002-2x250-b38.recalibrated.haplotypeCalls.vcf.gz	GRCh38	small-variants	SNP	7	chr7	152101382	152404297	331	FP	T	C	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:3374.77:FP:.:ti:SNP:het 	unsure	unsure	The variant is missing from the HiFi Asm, but PacBio and ONT seem to support it, although the region has high rate of polymorphism.	yes	no	in region of many FPs due to mismapped reads from extra regions in HG002 that are missing in GRCh38 so are mismapped to KMT2C																												152101382
NYGC	HG-002-2x250-b37.recalibrated.haplotypeCalls.vcf.gz	GRCh37	small-variants	SNP	7	chr7	152101713	152404628	3	FP	T	A	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:1017.77:FP:.:tv:SNP:het 	yes	no																															7:152101713	152404628
Common		GRCh38			7	chr7	152101716	152404631	1288	FP	C	CAAAAAAAAAA,CAAAAAAAAAAA,CAAAAAAAAAAAA	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:8.9675:FP:.:i6_15:INDEL:het	CommonFP			yes	no	in region of many FPs due to mismapped reads from extra regions in HG002 that are missing in GRCh38 so are mismapped to KMT2C													.:.:.:.:.:NOCALL:nocall	0/2:2148.73:FP:.:i6_15:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:1633.77:FP:.:i6_15:INDEL:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/3:3.4:FP:.:i6_15:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:.:i6_15:INDEL:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.		152101716
Common		GRCh38			7	chr7	152103004	152405919	12	FP	G	A	GT:QQ:BD:BK:BI:BVT:BLT	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	CommonFP			yes	no	in region of many FPs due to mismapped reads from extra regions in HG002 that are missing in GRCh38 so are mismapped to KMT2C													.:.:.:.:.:NOCALL:nocall	0/1:2973.77:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:4520.77:FP:.:ti:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:7.7:FP:.:ti:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:33.92:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:36:FP:.:ti:SNP:het		152103004
Common		GRCh38			7	chr7	152103016	152405931	57	FP	T	C	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:32.2195:FP:.:ti:SNP:het	CommonFP			yes	no	in region of many FPs due to mismapped reads from extra regions in HG002 that are missing in GRCh38 so are mismapped to KMT2C													.:.:.:.:.:NOCALL:nocall	0/1:2973.77:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:4674.77:FP:.:ti:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:7.9:FP:.:ti:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:48.37:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:27:FP:.:ti:SNP:het		152103016
Common		GRCh38			7	chr7	152103073	152405988	76	FP	CAG	C	GT:QQ:BD:BK:BI:BVT:BLT	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	CommonFP			yes	no	in region of many FPs due to mismapped reads from extra regions in HG002 that are missing in GRCh38 so are mismapped to KMT2C													.:.:.:.:.:NOCALL:nocall	0/1:498.73:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:740.73:FP:.:d1_5:INDEL:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:30.22:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:8:FP:.:d1_5:INDEL:het		152103073
Common		GRCh38			7	chr7	152103149	152406064	34	FP	G	A	GT:QQ:BD:BK:BI:BVT:BLT	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	CommonFP			yes	no	in region of many FPs due to mismapped reads from extra regions in HG002 that are missing in GRCh38 so are mismapped to KMT2C													.:.:.:.:.:NOCALL:nocall	0/1:516.77:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:830.77:FP:.:ti:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:28.17:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:20:FP:.:ti:SNP:het		152103149
Common		GRCh38			7	chr7	152103183	152406098	50	FP	T	A	GT:QQ:BD:BK:BI:BVT:BLT	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	CommonFP			yes	no	in region of many FPs due to mismapped reads from extra regions in HG002 that are missing in GRCh38 so are mismapped to KMT2C													.:.:.:.:.:NOCALL:nocall	0/1:283.77:FP:.:tv:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:3246.77:FP:.:tv:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:5.7:FP:.:tv:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:.:tv:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:50:FP:.:tv:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:24:FP:.:tv:SNP:het		152103183
Common		GRCh38			7	chr7	152103233	152406148	32	FP	G	T	GT:QQ:BD:BK:BI:BVT:BLT	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	CommonFP			yes	no	in region of many FPs due to mismapped reads from extra regions in HG002 that are missing in GRCh38 so are mismapped to KMT2C													.:.:.:.:.:NOCALL:nocall	0/1:740.77:FP:.:tv:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:2856.77:FP:.:tv:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:.:tv:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:27.39:FP:.:tv:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:29:FP:.:tv:SNP:het		152103233
Common		GRCh38			7	chr7	152103265	152406180	25	FP	G	A	GT:QQ:BD:BK:BI:BVT:BLT	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	CommonFP			yes	no	in region of many FPs due to mismapped reads from extra regions in HG002 that are missing in GRCh38 so are mismapped to KMT2C													.:.:.:.:.:NOCALL:nocall	0/1:456.77:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:686.77:FP:.:ti:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:22.23:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:11:FP:.:ti:SNP:het		152103265
CMH_DRAGEN_3.6.3	NA24385.hard-filtered.vcf.gz	GRCh38	small-variants	SNP	7	chr7	152103290	152406205	0	FP	G	A	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:45.15:FP:.:ti:SNP:het	unsure	unsure	In SINE. Although the query is better supported locally, the coverage profile is not uniform in the surrounding ~1kb window. I lean toward the truth from trio assembly but it is not well supported locally and I am unsure.	yes	no	in region of many FPs due to mismapped reads from extra regions in HG002 that are missing in GRCh38 so are mismapped to KMT2C						SINE. This looks like HET, 0/1 and appears to correlate with haplotype separation. Nearby variants also seem to be present on haplotypes that were not called.																						152103290
Common		GRCh38			7	chr7	152103290	152406205	119	FP	G	A	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:18.775:FP:.:ti:SNP:het	CommonFP			yes	no	in region of many FPs due to mismapped reads from extra regions in HG002 that are missing in GRCh38 so are mismapped to KMT2C													.:.:.:.:.:NOCALL:nocall	0/1:2091.77:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:7289.77:FP:.:ti:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:15.6:FP:.:ti:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:45.15:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:22:FP:.:ti:SNP:het		152103290
Common		GRCh38			7	chr7	152103409	152406324	55	FP	T	C	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:39.9993:FP:.:ti:SNP:het	CommonFP			yes	no	in region of many FPs due to mismapped reads from extra regions in HG002 that are missing in GRCh38 so are mismapped to KMT2C													.:.:.:.:.:NOCALL:nocall	0/1:4277.77:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:6349.77:FP:.:ti:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:4.7:FP:.:ti:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:22:FP:.:ti:SNP:het		152103409
Common		GRCh38			7	chr7	152103464	152406379	248	FP	C	G	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:.:tv:SNP:het	CommonFP			yes	no	in region of many FPs due to mismapped reads from extra regions in HG002 that are missing in GRCh38 so are mismapped to KMT2C													.:.:.:.:.:NOCALL:nocall	0/1:4235.77:FP:.:tv:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:6899.77:FP:.:tv:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:6.2:FP:.:tv:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:7:FP:.:tv:SNP:het		152103464
Common		GRCh38			7	chr7	152103712	152406627	106	FP	C	T	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:35.2289:FP:.:ti:SNP:het	CommonFP			yes	no	in region of many FPs due to mismapped reads from extra regions in HG002 that are missing in GRCh38 so are mismapped to KMT2C													.:.:.:.:.:NOCALL:nocall	0/1:1791.77:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:6709.77:FP:.:ti:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:79.6:FP:.:ti:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:16:FP:.:ti:SNP:het		152103712
BCM-HGSC_xAtlas	HG002.hs37d5.60x.1_merged.vcf.gz	GRCh37	small-variants	SNP	7	chr7	152103818	152406733	25	FP	C	T	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:10:FP:.:ti:SNP:het 	Yes	No																															7:152103818	152406733
Common		GRCh38			7	chr7	152103843	152406758	1899	FP	C	T	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:.:ti:SNP:het	CommonFP			yes	no	in region of many FPs due to mismapped reads from extra regions in HG002 that are missing in GRCh38 so are mismapped to KMT2C													.:.:.:.:.:NOCALL:nocall	0/1:1794.77:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:5637.77:FP:.:ti:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:212.6:FP:.:ti:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:5:FP:.:ti:SNP:het		152103843
NYGC	HG-002-2x250-b37.recalibrated.haplotypeCalls.vcf.gz	GRCh37	small-variants	SNP	7	chr7	152105742	152408657	749	FP	C	T	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:7039.77:FP:.:ti:SNP:het 	yes	no																															7:152105742	152408657
NYGC	HG-002-2x250-b37.recalibrated.haplotypeCalls.vcf.gz	GRCh37	small-variants	INDEL	7	chr7	152106491	152409406	788	FP	GAAGA	G	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:5999.73:FP:.:d1_5:INDEL:het 	yes	no																															7:152106491	152409406
PacBio_gatk4	gatk4hc_HG002_15kb_20kb_53X_SequelII.vcf.gz	GRCh38	small-variants	INDEL	7	chr7	152107279	152410194	134	FP	GA	G	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:936.73:FP:.:d1_5:INDEL:het	yes	no		yes	no	in region of many FPs due to mismapped reads from extra regions in HG002 that are missing in GRCh38 so are mismapped to KMT2C				skip																								152107279
NYGC	HG-002-2x250-b37.recalibrated.haplotypeCalls.vcf.gz	GRCh37	small-variants	SNP	7	chr7	152107413	152410328	563	FP	C	T	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:443.77:FP:.:ti:SNP:het 	yes	no																															7:152107413	152410328
PacBio_gatk4	gatk4hc_HG002_15kb_20kb_53X_SequelII.vcf.gz	GRCh38	small-variants	SNP	7	chr7	152107976	152410891	750	FP_FN	C	G	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:tv:SNP:homalt	0/1:FP:am:1462.77:tv:SNP:het	yes	no		yes	no	in region of many FPs due to mismapped reads from extra regions in HG002 that are missing in GRCh38 so are mismapped to KMT2C				skip																								152107976
PacBio_gatk4	gatk4hc_HG002_15kb_20kb_53X_SequelII.vcf.gz	GRCh38	small-variants	SNP	7	chr7	152108726	152411641	168	FP	T	G	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:735.77:FP:.:tv:SNP:het	yes	no		yes	no	in region of many FPs due to mismapped reads from extra regions in HG002 that are missing in GRCh38 so are mismapped to KMT2C				skip																								152108726
Common		GRCh38			7	chr7	152108894	152411809	461	FP	G	A	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:36.9903:FP:.:ti:SNP:het	CommonFP			yes	no	in region of many FPs due to mismapped reads from extra regions in HG002 that are missing in GRCh38 so are mismapped to KMT2C													.:.:.:.:.:NOCALL:nocall	0/1:1984.77:FP:.:ti:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:30.5:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:.:ti:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:36:FP:.:ti:SNP:het		152108894
Roche	RN_HG002_Illumina_PacBio_Oxford.vcf.gz	GRCh38	small-variants	SNP	7	chr7	152109355	152412270	139	FP	A	G	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:8.4389:FP:.:ti:SNP:het 	no	yes	from PB/ONT it seems this is real along with others in the cluster (the neighboring variants at chr7-152412265-G-A, chr7-152412279-T-G,), it is <10K segdup region so, PB/ONT should be able to call	yes	no	in region of many FPs due to mismapped reads from extra regions in HG002 that are missing in GRCh38 so are mismapped to KMT2C																												152109355
Roche	RN_HG002_Illumina_PacBio_Oxford.vcf.gz	GRCh38	small-variants	SNP	7	chr7	152109494	152412409	1112	FP	A	T	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	1/1:27.448:FP:.:tv:SNP:homalt 	no	yes	from PB/ONT it seems this is real along with others in the cluster (the neighboring variants at chr7-152412405-A-C, chr7-152412416-T-A, chr7-152412424-C-T,), it is <10K segdup region so, PB/ONT should be able to call	yes	no	in region of many FPs due to mismapped reads from extra regions in HG002 that are missing in GRCh38 so are mismapped to KMT2C																												152109494
PacBio_gatk4	gatk4hc_HG002_15kb_20kb_53X_SequelII.vcf.gz	GRCh38	small-variants	INDEL	7	chr7	152110606	152413521	1329	FP	C	CTGTAA	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:1365.73:FP:.:i1_5:INDEL:het	yes	no		yes	no	in region of many FPs due to mismapped reads from extra regions in HG002 that are missing in GRCh38 so are mismapped to KMT2C				skip																								152110606
ITER	ITERteam_small-variation_GRCh38_ILMN-PB-ONT.vcf.gz	GRCh38	small-variants	INDEL	7	chr7	152111935	152414850	659	FP	C	CT	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:6.2:FP:.:i1_5:INDEL:het	Yes	No		yes	no	in region of many FPs due to mismapped reads from extra regions in HG002 that are missing in GRCh38 so are mismapped to KMT2C				skip																								152111935
PacBio_gatk4	gatk4hc_HG002_15kb_20kb_53X_SequelII.vcf.gz	GRCh38	small-variants	SNP	7	chr7	152112594	152415509	67	FP	G	A	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:103.77:FP:.:ti:SNP:het	yes	no		yes	no	in region of many FPs due to mismapped reads from extra regions in HG002 that are missing in GRCh38 so are mismapped to KMT2C				skip																								152112594
PacBio_gatk4	gatk4hc_HG002_15kb_20kb_53X_SequelII.vcf.gz	GRCh38	small-variants	SNP	7	chr7	152112661	152415576	1472	FP	T	C	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100.77:FP:.:ti:SNP:het	yes	no		yes	no	in region of many FPs due to mismapped reads from extra regions in HG002 that are missing in GRCh38 so are mismapped to KMT2C				skip																								152112661
Common		GRCh37			7	chr7	152114133	152417048	0	FN	C	CA	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	in region of many FPs due to mismapped reads from extra regions in HG002 that are missing in GRCh38 so are mismapped to KMT2C													1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	7:152114133	152417048
Common		GRCh38			7	chr7	152114133	152417048	-150468030	FN	C	CA	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	in region of many FPs due to mismapped reads from extra regions in HG002 that are missing in GRCh38 so are mismapped to KMT2C													1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0		152114133
BCM-HGSC_xAtlas	HG002.hs37d5.60x.1_merged.vcf.gz	GRCh37	small-variants	INDEL	8	chr8	1897184	1949018	40325767	FN	ATG	A,ATGTGTG	GT:BD:BK:BI:BVT:BLT:QQ	1|2:FN:am:d1_5,i1_5:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:17 	Yes	No																															8:1897184	1949018
Roche	RN_HG002_Illumina_PacBio_Oxford_GRCh37.vcf.gz	GRCh37	small-variants	INDEL	8	chr8	42132303	42274785	1	FP	C	CGGGG	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:lm:i1_5:INDEL:het 	yes	no																															8:42132303	42274785
NCBI	HG002_grch37_dipcall.vcf.gz	GRCh37	small-variants	INDEL	8	chr8	42132304	42274786	13604	FP_FN	G	GC,GCC	GT:BD:BK:QQ:BI:BVT:BLT	2|2:FN:lm:.:i1_5:INDEL:homalt	1/1:FP:lm:30:i1_5:INDEL:homalt	unsure	unsure	evidence for various Cs INS here; repeat region	unsure	unsure	all techs noisy in long C homopolymer																											8:42132304	42274786
Common		GRCh37			8	chr8	42145908	42288390	0	FP_FN	CA	C	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:100:d1_5:INDEL:het	CommonFP_FN			no	yes	hifiasm misses ref haplotype in homopolymer due to highly homozygous region													1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:317.73:d1_5:INDEL:het	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:285.73:d1_5:INDEL:het	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:30:d1_5:INDEL:het	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:171.64:d1_5:INDEL:het	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:0:d1_5:INDEL:het	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:46.39:d1_5:INDEL:het	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:8:d1_5:INDEL:het	8:42145908	42288390
Common		GRCh38			8	chr8	42145908	42288390	39376499	FP_FN	CA	C	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:100:d1_5:INDEL:het	CommonFP_FN			no	yes	hifiasm misses ref haplotype in homopolymer due to highly homozygous region													1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:317.73:d1_5:INDEL:het	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:285.73:d1_5:INDEL:het	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:30:d1_5:INDEL:het	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:210.6:d1_5:INDEL:het	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:0:d1_5:INDEL:het	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:46.05:d1_5:INDEL:het	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:8:d1_5:INDEL:het		42145908
Common		GRCh37			8	chr8	82577124	81664889	0	FN	G	GA	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no	yes	likely hifiasm error in long homopolymer due to noisy HiFi reads													1|0:TP:gm:i1_5:INDEL:het:150.73	0/1:TP:gm:i1_5:INDEL:het:150.73	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	8:82577124	81664889
Common		GRCh38			8	chr8	82577124	81664889	12503208	FN	G	GA	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no	yes	likely hifiasm error in long homopolymer due to noisy HiFi reads													1|0:TP:gm:i1_5:INDEL:het:150.73	0/1:TP:gm:i1_5:INDEL:het:150.73	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0		82577124
Common		GRCh37			8	chr8	95180325	94168097	0	FP_FN	AATATATATATATATATATATATATATAT	A,AATATATATATATATATATATATATATATAT	GT:BD:BK:BI:BVT:BLT:QQ	2|1:FN:am:d16_plus,i1_5:INDEL:hetalt:.	0/1:FP:am:d16_plus:INDEL:het:100	CommonFP_FN			no	yes	likely hifiasm error in diTR calling 2bp ins instead of 4bp ins due to noisy HiFi reads													2|1:FN:am:d16_plus,i1_5:INDEL:hetalt:.	0/1:FP:am:d16_plus:INDEL:het:1257.73	2|1:FN:am:d16_plus,i1_5:INDEL:hetalt:.	0/1:FP:am:d16_plus:INDEL:het:665.73	2|1:FN:am:d16_plus,i1_5:INDEL:hetalt:.	0/1:FP:am:d16_plus:INDEL:het:30	2|1:FN:am:d16_plus,i1_5:INDEL:hetalt:.	0/1:FP:am:d16_plus:INDEL:het:688.06	2|1:FN:am:d16_plus,i1_5:INDEL:hetalt:.	0/1:FP:am:d16_plus:INDEL:het:0	2|1:FN:am:d16_plus,i1_5:INDEL:hetalt:.	0/1:FP:am:d16_plus:INDEL:het:50.02	2|1:FN:lm:d16_plus,i1_5:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:9	8:95180325	94168097
Common		GRCh38			8	chr8	95180325	94168097	49046820	FP_FN	AATATATATATATATATATATATATATAT	A,AATATATATATATATATATATATATATATAT	GT:BD:BK:BI:QQ:BVT:BLT	2|1:FN:am:d16_plus,i1_5:.:INDEL:hetalt	0/1:FP:am:d16_plus:100:INDEL:het	CommonFP_FN			no	yes	likely hifiasm error in diTR calling 2bp ins instead of 4bp ins due to noisy HiFi reads													2|1:FN:am:d16_plus,i1_5:.:INDEL:hetalt	0/1:FP:am:d16_plus:1257.73:INDEL:het	2|1:FN:am:d16_plus,i1_5:.:INDEL:hetalt	0/1:FP:am:d16_plus:584.27:INDEL:het	2|1:FN:am:d16_plus,i1_5:.:INDEL:hetalt	0/1:FP:am:d16_plus:30:INDEL:het	2|1:FN:am:d16_plus,i1_5:.:INDEL:hetalt	0/1:FP:am:d16_plus:335.06:INDEL:het	2|1:FN:am:d16_plus,i1_5:.:INDEL:hetalt	0/1:FP:am:d16_plus:0:INDEL:het	2|1:FN:am:d16_plus,i1_5:.:INDEL:hetalt	0/1:FP:am:d16_plus:50.02:INDEL:het	2|1:FN:lm:d16_plus,i1_5:.:INDEL:hetalt	.:.:.:.:9:NOCALL:nocall		95180325
Common		GRCh37			8	chr8	144296792	143214917	0	FN	GGCTTTGGGAGCA	G	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:.:d6_15:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no	yes	likely hifiasm consensus error since no evidence across techs													0|1:FN:.:d6_15:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d6_15:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d6_15:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d6_15:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d6_15:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d6_15:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d6_15:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	8:144296792	143214917
Common		GRCh38			8	chr8	144296792	143214917	1188	FN	GGCTTTGGGAGCA	G	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:.:d6_15:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no	yes	likely hifiasm consensus error since no evidence across techs													0|1:FN:.:d6_15:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d6_15:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d6_15:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d6_15:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d6_15:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d6_15:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d6_15:INDEL:het:.	.:.:.:.:NOCALL:nocall:0		144296792
Common		GRCh37			8	chr8	144297980	143216105	0	FP_FN	C	CG,CGG	GT:BD:BK:BI:QQ:BVT:BLT	2|1:FN:am:i1_5:.:INDEL:hetalt	0/1:FP:am:i1_5:100:INDEL:het	CommonFP_FN			unsure	unsure	all techs are noisy in G homopolymer													2|1:FN:am:i1_5:.:INDEL:hetalt	0/1:FP:am:i1_5:397.73:INDEL:het	2|1:FN:am:i1_5:.:INDEL:hetalt	0/1:FP:am:i1_5:83.73:INDEL:het	2|1:FN:am:i1_5:.:INDEL:hetalt	1/1:FP:am:i1_5:30:INDEL:homalt	2|1:FN:.:i1_5:.:INDEL:hetalt	.:.:.:.:0:NOCALL:nocall	2|1:FN:am:i1_5:.:INDEL:hetalt	0/1:FP:am:i1_5:0:INDEL:het	2|1:FN:am:i1_5:.:INDEL:hetalt	0/1:FP:am:i1_5:50:INDEL:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	8:144297980	143216105
Common		GRCh38			8	chr8	144297980	143216105	-108574412	FP_FN	C	CG,CGG	GT:BD:BK:BI:QQ:BVT:BLT	2|1:FN:am:i1_5:.:INDEL:hetalt	0/1:FP:am:i1_5:100:INDEL:het	CommonFP_FN			unsure	unsure	all techs are noisy in G homopolymer													2|1:FN:am:i1_5:.:INDEL:hetalt	0/1:FP:am:i1_5:397.73:INDEL:het	2|1:FN:.:i1_5:.:INDEL:hetalt	.:.:.:.:0:NOCALL:nocall	2|1:FN:am:i1_5:.:INDEL:hetalt	1/1:FP:am:i1_5:30:INDEL:homalt	2|1:FN:am:i1_5:.:INDEL:hetalt	0/1:FP:am:i1_5:76.64:INDEL:het	2|1:FN:am:i1_5:.:INDEL:hetalt	0/1:FP:am:i1_5:0:INDEL:het	2|1:FN:am:i1_5:.:INDEL:hetalt	0/1:FP:am:i1_5:50:INDEL:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.		144297980
Common		GRCh37			9	chr9	34641690	34641693	0	FP_FN	C	CT,CTT	GT:BD:BK:QQ:BI:BVT:BLT	0|2:FN:lm:.:i1_5:INDEL:het	0/1:FP:lm:100:i1_5:INDEL:het	CommonFP_FN			no	yes	likely hifiasm error in long homopolymer due to noisy HiFi reads													0|2:FN:.:.:i1_5:INDEL:het	.:.:.:0:.:NOCALL:nocall	0|2:FN:lm:.:i1_5:INDEL:het	0/1:FP:lm:250.73:i1_5:INDEL:het	0|2:FN:lm:.:i1_5:INDEL:het	1/1:FP:lm:30:i1_5:INDEL:homalt	0|2:FN:lm:.:i1_5:INDEL:het	0/1:FP:lm:51.64:i1_5:INDEL:het	0|2:FN:.:.:i1_5:INDEL:het	.:.:.:0:.:NOCALL:nocall	0|2:FN:lm:.:i1_5:INDEL:het	0/1:FP:lm:50:i1_5:INDEL:het	0|2:FN:lm:.:i1_5:INDEL:het	0/1:FP:lm:8:i1_5:INDEL:het	9:34641690	34641693
Common		GRCh38			9	chr9	34641690	34641693	8589	FP_FN	C	CT,CTT	GT:BD:BK:QQ:BI:BVT:BLT	0|2:FN:lm:.:i1_5:INDEL:het	0/1:FP:lm:100:i1_5:INDEL:het	CommonFP_FN			no	yes	likely hifiasm error in long homopolymer due to noisy HiFi reads													0|2:FN:.:.:i1_5:INDEL:het	.:.:.:0:.:NOCALL:nocall	0|2:FN:lm:.:i1_5:INDEL:het	0/1:FP:lm:252.73:i1_5:INDEL:het	0|2:FN:lm:.:i1_5:INDEL:het	1/1:FP:lm:30:i1_5:INDEL:homalt	0|2:FN:lm:.:i1_5:INDEL:het	0/1:FP:lm:94.64:i1_5:INDEL:het	0|2:FN:.:.:i1_5:INDEL:het	.:.:.:0:.:NOCALL:nocall	0|2:FN:lm:.:i1_5:INDEL:het	0/1:FP:lm:50:i1_5:INDEL:het	0|2:FN:lm:.:i1_5:INDEL:het	0/1:FP:lm:8:i1_5:INDEL:het		34641690
Common		GRCh37			9	chr9	34650279	34650282	34415258	FP_FN	C	CAAAAAAAAAAA,CAAAAAAAAA,CAAAAA,CAAAAAAAA,CAAAAAAAAAA	GT:BD:BK:BI:QQ:BVT:BLT	2|1:TP:gm:i6_15:100:INDEL:hetalt	1/2:TP:gm:i6_15:100:INDEL:hetalt	CommonFP_FN			yes	no	Illumina supports benchmark's long ins in long homopolymer													2|1:FN:.:i6_15:.:INDEL:hetalt	.:.:.:.:0:NOCALL:nocall	2|1:FN:am:i6_15:.:INDEL:hetalt	2/2:FP:am:i6_15:430.73:INDEL:homalt	2|1:FN:lm:i6_15:.:INDEL:hetalt	5/5:FP:lm:i6_15:30:INDEL:homalt	2|1:FN:lm:i6_15:.:INDEL:hetalt	4/3:FP:lm:i1_5,i6_15:11.2:INDEL:hetalt	2|1:FN:am:i6_15:.:INDEL:hetalt	2/2:FP:am:i6_15:0:INDEL:homalt	2|1:TP:gm:i6_15:193.59:INDEL:hetalt	1/2:TP:gm:i6_15:193.59:INDEL:hetalt	2|1:FN:am:i6_15:.:INDEL:hetalt	1/1:FP:am:i6_15:8:INDEL:homalt	9:34650279	34650282
BCM-HGSC_xAtlas	HG002.hs37d5.60x.1_merged.vcf.gz	GRCh37	small-variants	INDEL	9	chr9	71680456	69065540	116125	FP_FN	C	CAA,CAAA	GT:BD:BK:BI:QQ:BVT:BLT	1|2:FN:am:i1_5:.:INDEL:hetalt	1/1:FP:am:i1_5:15:INDEL:homalt 	Yes	No																															9:71680456	69065540
DNAnexus	GRCh38_HG002_WGS_union.vcf.gz	GRCh38	small-variants	SNP	9	chr9	71796581	69181665	15262	FP	A	T	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:.:tv:SNP:het 	yes 	no																																71796581
Common		GRCh37			9	chr9	71811843	69196927	0	FP	ATGTGTG	A	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	1/1:100:FP:lm:d6_15:INDEL:homalt	CommonFP			No		While the assembly is correct, a dipcall bug causes this insertion to be called without the adjacent deletion in the benchmark vcf, so should be excluded													.:.:.:.:.:NOCALL:nocall	1/1:2167.73:FP:lm:d6_15:INDEL:homalt	.:.:.:.:.:NOCALL:nocall	1/1:907.73:FP:lm:d6_15:INDEL:homalt	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	1/1:1201.03:FP:lm:d6_15:INDEL:homalt	.:.:.:.:.:NOCALL:nocall	1/1:0:FP:lm:d6_15:INDEL:homalt	.:.:.:.:.:NOCALL:nocall	1/1:95.58:FP:lm:d6_15:INDEL:homalt	.:.:.:.:.:NOCALL:nocall	1/1:13:FP:lm:d6_15:INDEL:homalt	9:71811843	69196927
Common		GRCh38			9	chr9	71811843	69196927	13	FP	ATGTGTG	A	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	1/1:39.9993:FP:lm:d6_15:INDEL:homalt	CommonFP			No		While the assembly is correct, a dipcall bug causes this insertion to be called without the adjacent deletion in the benchmark vcf, so should be excluded													.:.:.:.:.:NOCALL:nocall	1/1:2167.73:FP:lm:d6_15:INDEL:homalt	.:.:.:.:.:NOCALL:nocall	1/1:907.73:FP:lm:d6_15:INDEL:homalt	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	1/1:650.03:FP:lm:d6_15:INDEL:homalt	.:.:.:.:.:NOCALL:nocall	1/1:0:FP:lm:d6_15:INDEL:homalt	.:.:.:.:.:NOCALL:nocall	1/1:95.58:FP:lm:d6_15:INDEL:homalt	.:.:.:.:.:NOCALL:nocall	1/1:13:FP:lm:d6_15:INDEL:homalt		71811843
DNAnexus	GRCh38_HG002_WGS_union.vcf.gz	GRCh38	small-variants	INDEL	9	chr9	71811856	69196940	6	FP_FN	T	C,TACACACACAC,TACACACACACACACAC	GT:BD:BK:BI:QQ:BVT:BLT	2|3:FN:am:i16_plus,i6_15:.:INDEL:hetalt	1/0:FP:lm:ti:0:SNP:het 	unsure	unsure	Ins indicated by Pacbio, ONT and alignment based call, but Hom-ref by other techs	No		While the assembly is correct, a dipcall bug causes this insertion to be called without the adjacent deletion in the benchmark vcf, so should be excluded						LINE. ILMN, ONT (messy), HiFi support 10 & 16bp insert while 10X appears to support shorter insert.  If LINE how do you know what does with which LINE, that reads map to the correct LINE? Nearby variants do appear to correlate with this variant.  Unsure if REF allele is correct but other appears to be thus HET																						71811856
Common		GRCh37			9	chr9	71811862	69196946	0	FP	T	TACACACACACACACAC,TACACACACAC	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	1/2:100:FP:lm:i16_plus,i6_15:INDEL:hetalt	CommonFP			No		While the assembly is correct, a dipcall bug causes this insertion to be called without the adjacent deletion in the benchmark vcf, so should be excluded													.:.:.:.:.:NOCALL:nocall	1/2:1954.73:FP:lm:i16_plus,i6_15:INDEL:hetalt	.:.:.:.:.:NOCALL:nocall	1/2:1066.73:FP:lm:i16_plus,i6_15:INDEL:hetalt	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	1/2:1278.1:FP:lm:i16_plus,i6_15:INDEL:hetalt	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:lm:i16_plus:INDEL:het	.:.:.:.:.:NOCALL:nocall	1/2:170.62:FP:lm:i16_plus,i6_15:INDEL:hetalt	.:.:.:.:.:NOCALL:nocall	1/1:13:FP:lm:i16_plus:INDEL:homalt	9:71811862	69196946
Common		GRCh38			9	chr9	71811862	69196946	1213	FP	T	TACACACACAC,TACACACACACACACAC	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	2/1:100:FP:lm:i16_plus,i6_15:INDEL:hetalt	CommonFP			No		While the assembly is correct, a dipcall bug causes this insertion to be called without the adjacent deletion in the benchmark vcf, so should be excluded													.:.:.:.:.:NOCALL:nocall	2/1:1954.73:FP:lm:i16_plus,i6_15:INDEL:hetalt	.:.:.:.:.:NOCALL:nocall	2/1:1066.73:FP:lm:i16_plus,i6_15:INDEL:hetalt	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	2/1:638.1:FP:lm:i16_plus,i6_15:INDEL:hetalt	.:.:.:.:.:NOCALL:nocall	0/2:0:FP:lm:i16_plus:INDEL:het	.:.:.:.:.:NOCALL:nocall	2/1:168.33:FP:lm:i16_plus,i6_15:INDEL:hetalt	.:.:.:.:.:NOCALL:nocall	2/2:13:FP:lm:i16_plus:INDEL:homalt		71811862
BCM-HGSC_xAtlas	HG002.GRCh38.60x.1_merged.vcf.gz	GRCh38	small-variants	INDEL	9	chr9	71813075	69198159	12139	FP_FN	T	TTG	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:13:i1_5:INDEL:het 	Yes	No								skip																								71813075
NYGC	HG-002-2x250-b37.recalibrated.haplotypeCalls.vcf.gz	GRCh37	small-variants	INDEL	9	chr9	71825214	69210298	1	FN	C	CAAA	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:lm:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0 	unsure		this is at the junction of a run of homopolymer C to a run of homopolymer A  	unsure	unsure	all techs noisy in adjacent C and A homopolymers																											9:71825214	69210298
Common		GRCh37			9	chr9	71825215	69210299	2403	FP_FN	C	A,CCCCA,CAAA,CCCA,CA	GT:BD:BK:BI:QQ:BVT:BLT	2|1:FN:am:i1_5,tv:.:INDEL:hetalt	0/1:FP:am:tv:100:SNP:het	CommonFP_FN			unsure	unsure	all techs noisy in adjacent C and A homopolymers													2|1:FN:lm:i1_5,tv:.:INDEL:hetalt	5/5:FP:lm:i1_5:434.73:INDEL:homalt	2|1:FN:am:i1_5,tv:.:INDEL:hetalt	0/1:FP:am:tv:136.77:SNP:het	2|1:FN:lm:i1_5,tv:.:INDEL:hetalt	3/5:FP:lm:i1_5:30:INDEL:hetalt	2|1:FN:am:i1_5,tv:.:INDEL:hetalt	1/1:FP:am:tv:189:SNP:homalt	2|1:FN:lm:i1_5,tv:.:INDEL:hetalt	0/3:FP:lm:i1_5:0:INDEL:het	2|1:FN:lm:i1_5,tv:.:INDEL:hetalt	4/3:FP:lm:i1_5:186.94:INDEL:hetalt	2|1:FN:am:i1_5,tv:.:INDEL:hetalt	0/1:FP:am:tv:26:SNP:het	9:71825215	69210299
ITER	ITERteam_small-variation_GRCh37_ILMN-PB-ONT.vcf.gz	GRCh37	small-variants	SNP	9	chr9	71827618	69212702	60473	FP	T	C	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	1/1:500:FP:lm:ti:SNP:homalt	No	Yes	Good support in truth by ILMN, 10x and PacBio technologies.	yes	no	likely a duplicate call in query since this is in the benchmark																											9:71827618	69212702
Roche	RN_HG002_Illumina_PacBio_Oxford.vcf.gz	GRCh38	small-variants	INDEL	9	chr9	71888091	69273175	0	FP_FN	TA	T	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:100:d1_5:INDEL:het 	unsure	unsure	seems het from ILM	no	yes	Likely an error in hifiasm in homopolymer due to region of high homozygosity - should likely be het 1bp del																												71888091
NYGC	HG-002-2x250-b38.recalibrated.haplotypeCalls.vcf.gz	GRCh38	small-variants	INDEL	9	chr9	71888091	69273175	0	FP_FN	TA	T	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:264.73:d1_5:INDEL:het 	yes	yes		no	yes	Likely an error in hifiasm in homopolymer due to region of high homozygosity - should likely be het 1bp del																												71888091
Common		GRCh38			9	chr9	71888091	69273175	41501691	FP_FN	TA	T	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:100:d1_5:INDEL:het	CommonFP_FN			no	yes	Likely an error in hifiasm in homopolymer due to region of high homozygosity - should likely be het 1bp del													1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:616.75:d1_5:INDEL:het	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:264.73:d1_5:INDEL:het	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:30:d1_5:INDEL:het	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:125.6:d1_5:INDEL:het	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:0:d1_5:INDEL:het	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:48.96:d1_5:INDEL:het	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:11:d1_5:INDEL:het		71888091
ITER	ITERteam_small-variation_GRCh37_ILMN-PB-ONT.vcf.gz	GRCh37	small-variants	SNP	9	chr9	113537146	110774866	17025	FP	T	C	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	1/1:1364.08:FP:am:ti:SNP:homalt	Unsure	Unsure	We both called it a mixed variant with a SNP and indel. This SNP is already included in this mixed variant.	yes	no	benchmark complex variant in diTRs is supported by all techs, though Illumina has 2 different representations of ins+SNV																											9:113537146	110774866
Common		GRCh37			9	chr9	113554171	110791891	0	FN	G	T	GT:BD:BK:BI:BVT:BLT:QQ	0|1:TP:gm:tv:SNP:het:100	0/1:TP:gm:tv:SNP:het:100	CommonFN			yes	no	region of several het calls in L1H missed by short reads													0|1:TP:gm:tv:SNP:het:967.77	0/1:TP:gm:tv:SNP:het:967.77	0|1:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:TP:gm:tv:SNP:het:500	0/1:TP:gm:tv:SNP:het:500	0|1:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	9:113554171	110791891
Common		GRCh38			9	chr9	113554171	110791891	720	FN	G	T	GT:BD:BK:QQ:BI:BVT:BLT	0|1:TP:gm:100:tv:SNP:het	0/1:TP:gm:100:tv:SNP:het	CommonFN			yes	no	region of several het calls in L1H missed by short reads													0|1:TP:gm:967.77:tv:SNP:het	0/1:TP:gm:967.77:tv:SNP:het	0|1:FN:.:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:.:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:TP:gm:500:tv:SNP:het	0/1:TP:gm:500:tv:SNP:het	0|1:FN:.:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:.:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:.:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall		113554171
Common		GRCh37			9	chr9	113554891	110792611	0	FN	T	C	GT:BD:BK:BI:BVT:BLT:QQ	0|1:TP:gm:ti:SNP:het:100	0/1:TP:gm:ti:SNP:het:100	CommonFN			yes	no	region of several het calls in L1H missed by short reads													0|1:TP:gm:ti:SNP:het:1011.77	0/1:TP:gm:ti:SNP:het:1011.77	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:TP:gm:ti:SNP:het:500	0/1:TP:gm:ti:SNP:het:500	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	9:113554891	110792611
Common		GRCh38			9	chr9	113554891	110792611	118	FN	T	C	GT:BD:BK:QQ:BI:BVT:BLT	0|1:TP:gm:100:ti:SNP:het	0/1:TP:gm:100:ti:SNP:het	CommonFN			yes	no	region of several het calls in L1H missed by short reads													0|1:TP:gm:1011.77:ti:SNP:het	0/1:TP:gm:1011.77:ti:SNP:het	0|1:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:TP:gm:500:ti:SNP:het	0/1:TP:gm:500:ti:SNP:het	0|1:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall		113554891
Common		GRCh37			9	chr9	113555009	110792729	0	FN	C	G	GT:BD:BK:BI:BVT:BLT:QQ	0|1:TP:gm:tv:SNP:het:100	0/1:TP:gm:tv:SNP:het:100	CommonFN			yes	no	region of several het calls in L1H missed by short reads													0|1:TP:gm:tv:SNP:het:972.77	0/1:TP:gm:tv:SNP:het:972.77	0|1:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:TP:gm:tv:SNP:het:500	0/1:TP:gm:tv:SNP:het:500	0|1:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	9:113555009	110792729
Common		GRCh38			9	chr9	113555009	110792729	234	FN	C	G	GT:BD:BK:QQ:BI:BVT:BLT	0|1:TP:gm:100:tv:SNP:het	0/1:TP:gm:100:tv:SNP:het	CommonFN			yes	no	region of several het calls in L1H missed by short reads													0|1:TP:gm:972.77:tv:SNP:het	0/1:TP:gm:972.77:tv:SNP:het	0|1:FN:.:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:.:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:TP:gm:500:tv:SNP:het	0/1:TP:gm:500:tv:SNP:het	0|1:FN:.:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:.:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:.:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall		113555009
Common		GRCh37			9	chr9	113555243	110792963	0	FN	A	G	GT:BD:BK:BI:BVT:BLT:QQ	0|1:TP:gm:ti:SNP:het:100	0/1:TP:gm:ti:SNP:het:100	CommonFN			yes	no	region of several het calls in L1H missed by short reads													0|1:TP:gm:ti:SNP:het:1076.77	0/1:TP:gm:ti:SNP:het:1076.77	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:TP:gm:ti:SNP:het:500	0/1:TP:gm:ti:SNP:het:500	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	9:113555243	110792963
Common		GRCh38			9	chr9	113555243	110792963	507	FN	A	G	GT:BD:BK:QQ:BI:BVT:BLT	0|1:TP:gm:100:ti:SNP:het	0/1:TP:gm:100:ti:SNP:het	CommonFN			yes	no	region of several het calls in L1H missed by short reads													0|1:TP:gm:1076.77:ti:SNP:het	0/1:TP:gm:1076.77:ti:SNP:het	0|1:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:TP:gm:500:ti:SNP:het	0/1:TP:gm:500:ti:SNP:het	0|1:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall		113555243
Common		GRCh37			9	chr9	113555750	110793470	0	FN	G	C	GT:BD:BK:BI:BVT:BLT:QQ	0|1:TP:gm:tv:SNP:het:26.2004	0/1:TP:gm:tv:SNP:het:26.2004	CommonFN			yes	no	region of several het calls in L1H missed by short reads													0|1:TP:gm:tv:SNP:het:1008.77	0/1:TP:gm:tv:SNP:het:1008.77	0|1:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:TP:gm:tv:SNP:het:500	0/1:TP:gm:tv:SNP:het:500	0|1:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	9:113555750	110793470
Common		GRCh38			9	chr9	113555750	110793470	1106	FN	G	C	GT:BD:BK:QQ:BI:BVT:BLT	0|1:TP:gm:18.2256:tv:SNP:het	0/1:TP:gm:18.2256:tv:SNP:het	CommonFN			yes	no	region of several het calls in L1H missed by short reads													0|1:TP:gm:1008.77:tv:SNP:het	0/1:TP:gm:1008.77:tv:SNP:het	0|1:FN:.:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:.:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:TP:gm:500:tv:SNP:het	0/1:TP:gm:500:tv:SNP:het	0|1:FN:.:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:.:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:.:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall		113555750
DNAnexus	hs37d5_HG002_WGS_union.vcf.gz	GRCh37	small-variants	SNP	9	chr9	113556856	110794576	22471996	FP	C	G	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:.:tv:SNP:het	yes	no																															9:113556856	110794576
Common		GRCh37			9	chr9	136141986	133266572	0	FP_FN	CT	C	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:100:d1_5:INDEL:het	CommonFP_FN			no	yes	Likely an error in hifiasm in homopolymer due to region of high homozygosity - should be 1bp and 2bp del													1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:435.73:d1_5:INDEL:het	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:299.73:d1_5:INDEL:het	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:30:d1_5:INDEL:het	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:493.6:d1_5:INDEL:het	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:0:d1_5:INDEL:het	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:47.95:d1_5:INDEL:het	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:11:d1_5:INDEL:het	9:136141986	133266572
DNAnexus	GRCh38_HG002_WGS_union.vcf.gz	GRCh38	small-variants	INDEL	9	chr9	136141986	133266572	0	FP_FN	CTT	C	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:0:d1_5:INDEL:het 	unsure	yes	It looks more like heterzygous deletion with deletion of one T and two T's.	no	yes	Likely an error in hifiasm in homopolymer due to region of high homozygosity - should be 1bp and 2bp del						LINE. Significant drop in coveraage for all techs at this site possibly implying reads belong somewhere else or that reads that go here mapped somewhere else.  Given what there is looks like one or two deletions of T, 10X and ILMN support this. However HiFI seems to support REF or 2 bp deletion.  ONT is less clear.  Nearby variants correspond to all possible alleles. Unsure of variant but appear to be HET.						Appears to be a 1-2bp deletion supported by Illumina and PacBio																136141986
Common		GRCh38			9	chr9	136141986	133266572	1	FP_FN	CTT	C	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:100:d1_5:INDEL:het	CommonFP_FN			no	yes	Likely an error in hifiasm in homopolymer due to region of high homozygosity - should be 1bp and 2bp del													1|1:FN:.:.:d1_5:INDEL:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:980.73:d1_5:INDEL:het	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:30:d1_5:INDEL:het	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:394.06:d1_5:INDEL:het	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:0:d1_5:INDEL:het	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:258.52:d1_5:INDEL:het	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:11:d1_5:INDEL:het		136141986
CMH_DRAGEN_3.6.3	NA24385.hard-filtered.vcf.gz	GRCh38	small-variants	INDEL	9	chr9	136141987	133266573	0	FP	TT	T	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:258.52:FP:lm:d1_5:INDEL:het	no	yes	The query is well supported by PacBio/ILMN and reads are aligned with high MQ, though in LINE.	no	yes	Likely an error in hifiasm in homopolymer due to region of high homozygosity - should be 1bp and 2bp del						LINE. Homopolymer T, truth has variant directly adjacent to this FP site. Most reads support 2 bp deletion however some  support REF and 1 or 3 deletions.  ONT is messy. Likely a HET but unsue of variants. 				no		Reads support a 2bp or 3bp deletion																136141987
Common		GRCh38			9	chr9	136141987	133266573	3840420	FP	TT	T	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:lm:d1_5:INDEL:het	CommonFP			no	yes	Likely an error in hifiasm in homopolymer due to region of high homozygosity - should be 1bp and 2bp del													./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:980.73:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:394.06:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:258.52:FP:lm:d1_5:INDEL:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.		136141987
Common		GRCh37			9	chr9	140001445	137106993	0	FN	TGGG	T	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no	yes	likely hifiasm consensus error since no evidence across techs													1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	9:140001445	137106993
Common		GRCh38			9	chr9	140001445	137106993	-122176679	FN	TGGG	T	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no	yes	likely hifiasm consensus error since no evidence across techs													1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0		140001445
ITER	ITERteam_small-variation_GRCh37_ILMN-PB-ONT.vcf.gz	GRCh37	small-variants	SNP	10	chr10	14972313	14930314	2879584	FP	G	T	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:65.6:FP:.:tv:SNP:het	Yes	No																															10:14972313	14930314
Common		GRCh37			10	chr10	18098887	17809898	72	FN	G	A	GT:BD:BK:BI:BVT:BLT:QQ	0|1:TP:gm:ti:SNP:het:36.989	0/1:TP:gm:ti:SNP:het:36.989	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:TP:gm:ti:SNP:het:30	0/1:TP:gm:ti:SNP:het:30	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	10:18098887	17809898
Common		GRCh37			10	chr10	18098959	17809970	95	FN	A	G	GT:BD:BK:BI:BVT:BLT:QQ	1|1:TP:gm:ti:SNP:homalt:100	1/1:TP:gm:ti:SNP:homalt:100	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:ti:SNP:homalt:30	1/1:TP:gm:ti:SNP:homalt:30	1|1:TP:gm:ti:SNP:homalt:7.2	1/1:TP:gm:ti:SNP:homalt:7.2	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	10:18098959	17809970
Common		GRCh37			10	chr10	18099054	17810065	80	FN	TAGAA	T	GT:BD:BK:BI:BVT:BLT:QQ	0|1:TP:gm:d1_5:INDEL:het:100	0/1:TP:gm:d1_5:INDEL:het:100	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:TP:gm:d1_5:INDEL:het:30	0/1:TP:gm:d1_5:INDEL:het:30	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	10:18099054	17810065
Common		GRCh37			10	chr10	18099134	17810145	972	FN	A	T	GT:BD:BK:BI:BVT:BLT:QQ	1|1:TP:gm:tv:SNP:homalt:100	1/1:TP:gm:tv:SNP:homalt:100	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:tv:SNP:homalt:30	1/1:TP:gm:tv:SNP:homalt:30	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	10:18099134	17810145
Common		GRCh37			10	chr10	18100106	17811117	401	FN	T	C	GT:BD:BK:BI:BVT:BLT:QQ	1|0:TP:gm:ti:SNP:het:100	0/1:TP:gm:ti:SNP:het:100	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:ti:SNP:het:30	0/1:TP:gm:ti:SNP:het:30	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	10:18100106	17811117
Common		GRCh37			10	chr10	18100507	17811518	235	FN	A	AC	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:TP:gm:i1_5:INDEL:het:30	0/1:TP:gm:i1_5:INDEL:het:30	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	10:18100507	17811518
Common		GRCh37			10	chr10	18100742	17811753	30	FN	A	T	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:tv:SNP:homalt:30	1/1:TP:gm:tv:SNP:homalt:30	1|1:FN:lm:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	10:18100742	17811753
Common		GRCh37			10	chr10	18100772	17811783	730	FN	A	C	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:tv:SNP:homalt:30	1/1:TP:gm:tv:SNP:homalt:30	1|1:TP:gm:tv:SNP:homalt:6.2	1/1:TP:gm:tv:SNP:homalt:6.2	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	10:18100772	17811783
Common		GRCh37			10	chr10	18101502	17812513	54	FN	A	G	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:ti:SNP:het:30	0/1:TP:gm:ti:SNP:het:30	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:lm:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	10:18101502	17812513
Common		GRCh37			10	chr10	18101556	17812567	419	FP_FN	C	CT,CTTT,CTT	GT:BD:BK:BI:QQ:BVT:BLT	2|1:FN:am:i1_5:.:INDEL:hetalt	1/1:FP:am:i1_5:18.6785:INDEL:homalt	CommonFP_FN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													2|1:FN:.:i1_5:.:INDEL:hetalt	.:.:.:.:0:NOCALL:nocall	2|1:FN:am:i1_5:.:INDEL:hetalt	1/1:FP:am:i1_5:45:INDEL:homalt	2|1:FN:lm:i1_5:.:INDEL:hetalt	3/3:FP:lm:i1_5:30:INDEL:homalt	2|1:FN:.:i1_5:.:INDEL:hetalt	.:.:.:.:0:NOCALL:nocall	2|1:FN:am:i1_5:.:INDEL:hetalt	1/1:FP:am:i1_5:0:INDEL:homalt	2|1:FN:.:i1_5:.:INDEL:hetalt	.:.:.:.:0:NOCALL:nocall	2|1:FN:am:i1_5:.:INDEL:hetalt	1/1:FP:am:i1_5:11:INDEL:homalt	10:18101556	17812567
Common		GRCh37			10	chr10	18101972	17812986	1431	FN	G	T	GT:BD:BK:BI:BVT:BLT:QQ	1|1:TP:gm:tv:SNP:homalt:27.2143	1/1:TP:gm:tv:SNP:homalt:27.2143	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:tv:SNP:homalt:30	1/1:TP:gm:tv:SNP:homalt:30	1|1:TP:gm:tv:SNP:homalt:9.5	1/1:TP:gm:tv:SNP:homalt:9.5	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	10:18101972	17812986
Common		GRCh37			10	chr10	18103401	17814417	47	FN	T	C	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:ti:SNP:het:30	0/1:TP:gm:ti:SNP:het:30	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	10:18103401	17814417
Common		GRCh37			10	chr10	18103448	17814464	3	FN	G	C	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:tv:SNP:het:30	0/1:TP:gm:tv:SNP:het:30	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	10:18103448	17814464
Common		GRCh37			10	chr10	18103451	17814467	595	FN	A	G	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:ti:SNP:het:30	0/1:TP:gm:ti:SNP:het:30	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	10:18103451	17814467
CMH_DRAGEN_3.6.3	NA24385.hard-filtered.vcf.gz	GRCh37	small-variants	SNP	10	chr10	18104047	17815062	0	FN	C	T	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	unsure	unsure	In segdup/selfchain. No good evident supporting the variants in any alignments	yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38																											10:18104047	17815062
Common		GRCh37			10	chr10	18104047	17815062	503	FN	C	T	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:ti:SNP:het:30	0/1:TP:gm:ti:SNP:het:30	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	10:18104047	17815062
Common		GRCh37			10	chr10	18104550	17815565	433	FN	A	T	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:lm:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:tv:SNP:het:30	0/1:TP:gm:tv:SNP:het:30	1|0:FN:lm:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:lm:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:lm:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	10:18104550	17815565
Roche	RN_HG002_Illumina_PacBio_Oxford_GRCh37.vcf.gz	GRCh37	small-variants	SNP	10	chr10	18104982	17815998	0	FN	G	A	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0 	unsure		not so clear from any of the technologies	yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38																											10:18104982	17815998
Common		GRCh37			10	chr10	18104982	17815998	27	FN	G	A	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:ti:SNP:het:30	0/1:TP:gm:ti:SNP:het:30	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	10:18104982	17815998
Common		GRCh37			10	chr10	18105009	17816025	913	FN	C	T	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:ti:SNP:het:30	0/1:TP:gm:ti:SNP:het:30	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	10:18105009	17816025
Common		GRCh37			10	chr10	18105922	17816938	255	FN	C	A	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:tv:SNP:het:30	0/1:TP:gm:tv:SNP:het:30	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	10:18105922	17816938
Common		GRCh37			10	chr10	18106177	17817193	258	FP_FN	C	T	GT:BD:BK:QQ:BI:BVT:BLT	0|1:FN:am:.:ti:SNP:het	1/1:FP:am:100:ti:SNP:homalt	CommonFP_FN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													0|1:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:am:.:ti:SNP:het	1/1:FP:am:523.77:ti:SNP:homalt	0|1:TP:gm:30:ti:SNP:het	0/1:TP:gm:30:ti:SNP:het	0|1:FN:am:.:ti:SNP:het	1/1:FP:am:14:ti:SNP:homalt	0|1:FN:am:.:ti:SNP:het	1/1:FP:am:0:ti:SNP:homalt	0|1:FN:am:.:ti:SNP:het	1/1:FP:am:37.6:ti:SNP:homalt	0|1:FN:am:.:ti:SNP:het	1/1:FP:am:33:ti:SNP:homalt	10:18106177	17817193
Common		GRCh37			10	chr10	18106434	17817451	243	FN	C	T	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:ti:SNP:het:30	0/1:TP:gm:ti:SNP:het:30	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	10:18106434	17817451
Common		GRCh37			10	chr10	18106677	17817694	570	FN	T	A	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:tv:SNP:het:30	0/1:TP:gm:tv:SNP:het:30	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	10:18106677	17817694
Common		GRCh37			10	chr10	18107247	17818264	58	FN	C	T	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:ti:SNP:het:30	0/1:TP:gm:ti:SNP:het:30	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	10:18107247	17818264
Common		GRCh37			10	chr10	18107305	17818322	492	FN	G	A	GT:BD:BK:BI:BVT:BLT:QQ	1|1:TP:gm:ti:SNP:homalt:100	1/1:TP:gm:ti:SNP:homalt:100	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:ti:SNP:homalt:30	1/1:TP:gm:ti:SNP:homalt:30	1|1:TP:gm:ti:SNP:homalt:21.3	1/1:TP:gm:ti:SNP:homalt:21.3	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	10:18107305	17818322
Common		GRCh37			10	chr10	18107797	17818814	254	FN	C	A	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:lm:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:10.2299	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:tv:SNP:homalt:30	1/1:TP:gm:tv:SNP:homalt:30	1|1:TP:gm:tv:SNP:homalt:15	1/1:TP:gm:tv:SNP:homalt:15	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	10:18107797	17818814
Common		GRCh37			10	chr10	18108051	17819068	785	FN	A	G	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:ti:SNP:het:30	0/1:TP:gm:ti:SNP:het:30	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	10:18108051	17819068
Common		GRCh37			10	chr10	18108824	17819853	170	FN	G	C	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:tv:SNP:het:30	0/1:TP:gm:tv:SNP:het:30	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	10:18108824	17819853
Common		GRCh37			10	chr10	18108994	17820023	1015	FN	C	G	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:tv:SNP:het:30	0/1:TP:gm:tv:SNP:het:30	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	10:18108994	17820023
Common		GRCh37			10	chr10	18110009	17821038	25	FN	C	T	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:lm:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:lm:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:ti:SNP:het:30	0/1:TP:gm:ti:SNP:het:30	1|0:FN:lm:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:lm:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:lm:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	10:18110009	17821038
Common		GRCh37			10	chr10	18110034	17821063	662	FN	A	T	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:lm:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:lm:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:tv:SNP:het:30	0/1:TP:gm:tv:SNP:het:30	1|0:FN:lm:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:lm:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:lm:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	10:18110034	17821063
Common		GRCh37			10	chr10	18110695	17821725	296	FN	A	T	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:tv:SNP:het:30	0/1:TP:gm:tv:SNP:het:30	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:lm:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	10:18110695	17821725
Common		GRCh37			10	chr10	18110991	17822021	327	FN	G	A	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:ti:SNP:het:30	0/1:TP:gm:ti:SNP:het:30	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	10:18110991	17822021
Common		GRCh37			10	chr10	18111318	17822348	907	FN	A	G	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:ti:SNP:het:30	0/1:TP:gm:ti:SNP:het:30	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	10:18111318	17822348
Common		GRCh37			10	chr10	18112225	17823255	395	FN	A	G	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:ti:SNP:het:30	0/1:TP:gm:ti:SNP:het:30	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	10:18112225	17823255
Common		GRCh37			10	chr10	18112620	17823650	292	FN	G	A	GT:BD:BK:BI:BVT:BLT:QQ	1|1:TP:gm:ti:SNP:homalt:100	1/1:TP:gm:ti:SNP:homalt:100	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:ti:SNP:homalt:30	1/1:TP:gm:ti:SNP:homalt:30	1|1:TP:gm:ti:SNP:homalt:22	1/1:TP:gm:ti:SNP:homalt:22	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	10:18112620	17823650
Common		GRCh37			10	chr10	18112912	17823942	85	FP_FN	C	T	GT:BD:BK:QQ:BI:BVT:BLT	0|1:FN:am:.:ti:SNP:het	1/1:FP:am:39.9993:ti:SNP:homalt	CommonFP_FN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													0|1:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:am:.:ti:SNP:het	1/1:FP:am:500.77:ti:SNP:homalt	0|1:TP:gm:30:ti:SNP:het	0/1:TP:gm:30:ti:SNP:het	0|1:FN:am:.:ti:SNP:het	1/1:FP:am:23.6:ti:SNP:homalt	0|1:FN:am:.:ti:SNP:het	1/1:FP:am:0:ti:SNP:homalt	0|1:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:am:.:ti:SNP:het	1/1:FP:am:36:ti:SNP:homalt	10:18112912	17823942
Common		GRCh37			10	chr10	18112997	17824027	1328	FN	A	C	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:tv:SNP:het:30	0/1:TP:gm:tv:SNP:het:30	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	10:18112997	17824027
Common		GRCh37			10	chr10	18114325	17825355	842	FN	A	G	GT:BD:BK:BI:BVT:BLT:QQ	0|1:TP:gm:ti:SNP:het:100	0/1:TP:gm:ti:SNP:het:100	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:TP:gm:ti:SNP:het:30	0/1:TP:gm:ti:SNP:het:30	0|1:TP:gm:ti:SNP:het:6.7	0/1:TP:gm:ti:SNP:het:6.7	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	10:18114325	17825355
Common		GRCh37			10	chr10	18115167	17826197	292	FN	C	CT	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:i1_5:INDEL:het:30	0/1:TP:gm:i1_5:INDEL:het:30	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	10:18115167	17826197
ITER	ITERteam_small-variation_GRCh37_ILMN-PB-ONT.vcf.gz	GRCh37	small-variants	SNP	10	chr10	18115458	17826489	0	FN	C	A	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	No	Yes	Few reads support this variant (only 1 read for 10X and 3 for ONT, both with low MQ).	yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38																											10:18115458	17826489
Common		GRCh37			10	chr10	18115458	17826489	42	FN	C	A	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:tv:SNP:het:30	0/1:TP:gm:tv:SNP:het:30	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	10:18115458	17826489
Common		GRCh37			10	chr10	18115500	17826531	966	FN	TGAA	T	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:d1_5:INDEL:het:30	0/1:TP:gm:d1_5:INDEL:het:30	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	10:18115500	17826531
DNAnexus	hs37d5_HG002_WGS_union.vcf.gz	GRCh37	small-variants	SNP	10	chr10	18116450	17827497	0	FP_FN	G	A	GT:BD:BK:QQ:BI:BVT:BLT	0|1:FN:am:.:ti:SNP:het	1/1:FP:am:0:ti:SNP:homalt	no	yes	While one of the haplotype call this poistion as G, PacBio data have 18 reads aligned to this poition and it is all A's, suggesting this position is likley homozygous alt. Also, three short read variant callers (DeepVariant, Sentieon, and Strelka2) calling this locus as homozygous alt (A/A).	yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38																											10:18116450	17827497
CMH_DRAGEN_3.6.3	NA24385.hard-filtered.vcf.gz	GRCh37	small-variants	SNP	10	chr10	18116450	17827497	674	FP_FN	G	A	GT:BD:BK:QQ:BI:BVT:BLT	0|1:FN:am:.:ti:SNP:het	1/1:FP:am:49.73:ti:SNP:homalt	unsure	unsure	In segdup/selfchain. The query is much better supported than benchmark, but mapping quality is low in general and unsure about either	yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38																											10:18116450	17827497
PacBio_gatk4	gatk4hc_HG002_15kb_20kb_52X_SequelII.vcf.gz	GRCh37	small-variants	SNP	10	chr10	18117124	17828171	0	FN	G	A	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	unsure	unsure	no read support	yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38																											10:18117124	17828171
Common		GRCh37			10	chr10	18117124	17828171	689	FN	G	A	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:ti:SNP:het:30	0/1:TP:gm:ti:SNP:het:30	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	10:18117124	17828171
Common		GRCh37			10	chr10	18117813	17828860	239	FN	C	T	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:ti:SNP:het:30	0/1:TP:gm:ti:SNP:het:30	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	10:18117813	17828860
Roche	RN_HG002_Illumina_PacBio_Oxford_GRCh37.vcf.gz	GRCh37	small-variants	SNP	10	chr10	18118052	17829099	0	FP_FN	C	T	GT:BD:BK:QQ:BI:BVT:BLT	0|1:FN:am:.:ti:SNP:het	1/1:FP:am:100:ti:SNP:homalt 	yes	no		yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38																											10:18118052	17829099
NYGC	HG-002-2x250-b37.recalibrated.haplotypeCalls.vcf.gz	GRCh37	small-variants	SNP	10	chr10	18118052	17829099	174	FP_FN	C	T	GT:BD:BK:QQ:BI:BVT:BLT	0|1:FN:am:.:ti:SNP:het	1/1:FP:am:650.77:ti:SNP:homalt 	unsure	yes	Evidence for the het genotype only seen in Pacbio Hifi assembly. Not much evidence for het in CCS or Illumina, although coverage in Illumina is very low. The variant is in a seqdup region.	yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38																											10:18118052	17829099
Common		GRCh37			10	chr10	18118226	17829273	1340	FN	T	C	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:ti:SNP:het:30	0/1:TP:gm:ti:SNP:het:30	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:lm:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	10:18118226	17829273
Common		GRCh37			10	chr10	18119566	17830613	271	FN	C	T	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:ti:SNP:het:30	0/1:TP:gm:ti:SNP:het:30	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	10:18119566	17830613
Common		GRCh37			10	chr10	18119837	17830884	171	FN	C	CTA	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:i1_5:INDEL:het:30	0/1:TP:gm:i1_5:INDEL:het:30	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	10:18119837	17830884
Common		GRCh37			10	chr10	18120006	17831055	361	FN	AT	A	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:d1_5:INDEL:het:30	0/1:TP:gm:d1_5:INDEL:het:30	1|0:TP:gm:d1_5:INDEL:het:5.7	0/1:TP:gm:d1_5:INDEL:het:5.7	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	10:18120006	17831055
Common		GRCh37			10	chr10	18120368	17831416	292	FN	G	T	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:tv:SNP:het:30	0/1:TP:gm:tv:SNP:het:30	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	10:18120368	17831416
Common		GRCh37			10	chr10	18120660	17831708	892	FP_FN	A	T	GT:BD:BK:QQ:BI:BVT:BLT	0|1:FN:am:.:tv:SNP:het	1/1:FP:am:100:tv:SNP:homalt	CommonFP_FN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													0|1:FN:.:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:am:.:tv:SNP:het	1/1:FP:am:225.78:tv:SNP:homalt	0|1:TP:gm:30:tv:SNP:het	0/1:TP:gm:30:tv:SNP:het	0|1:FN:am:.:tv:SNP:het	1/1:FP:am:14.2:tv:SNP:homalt	0|1:FN:am:.:tv:SNP:het	1/1:FP:am:0:tv:SNP:homalt	0|1:FN:.:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:am:.:tv:SNP:het	1/1:FP:am:29:tv:SNP:homalt	10:18120660	17831708
Common		GRCh37			10	chr10	18121552	17832600	452	FN	T	G	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:tv:SNP:het:30	0/1:TP:gm:tv:SNP:het:30	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:lm:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	10:18121552	17832600
Common		GRCh37			10	chr10	18122004	17833052	468	FN	C	A	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:tv:SNP:het:30	0/1:TP:gm:tv:SNP:het:30	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	10:18122004	17833052
Common		GRCh37			10	chr10	18122472	17833520	243	FN	CA	C	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:d1_5:INDEL:het:30	0/1:TP:gm:d1_5:INDEL:het:30	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:lm:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	10:18122472	17833520
Common		GRCh37			10	chr10	18122716	17833763	54	FN	A	G	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:ti:SNP:het:30	0/1:TP:gm:ti:SNP:het:30	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	10:18122716	17833763
Common		GRCh37			10	chr10	18122770	17833817	26	FN	A	T	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:tv:SNP:het:30	0/1:TP:gm:tv:SNP:het:30	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:lm:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	10:18122770	17833817
Common		GRCh37			10	chr10	18122796	17833843	1	FN	G	A	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:ti:SNP:het:30	0/1:TP:gm:ti:SNP:het:30	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	10:18122796	17833843
Common		GRCh37			10	chr10	18122797	17833844	14	FN	T	G	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:tv:SNP:het:30	0/1:TP:gm:tv:SNP:het:30	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	10:18122797	17833844
Common		GRCh37			10	chr10	18122811	17833858	472	FN	G	T	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:tv:SNP:het:30	0/1:TP:gm:tv:SNP:het:30	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	10:18122811	17833858
DNAnexus	hs37d5_HG002_WGS_union.vcf.gz	GRCh37	small-variants	SNP	10	chr10	18123283	17834330	1221	FN	G	C	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	yes	no		yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38																											10:18123283	17834330
Common		GRCh37			10	chr10	18124504	17835551	459	FN	C	G	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:tv:SNP:het:30	0/1:TP:gm:tv:SNP:het:30	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	10:18124504	17835551
Common		GRCh37			10	chr10	18124963	17836010	281	FN	G	C	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:tv:SNP:het:30	0/1:TP:gm:tv:SNP:het:30	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	10:18124963	17836010
Common		GRCh37			10	chr10	18125244	17836291	292	FN	A	G	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:lm:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:lm:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:ti:SNP:het:30	0/1:TP:gm:ti:SNP:het:30	1|0:FN:lm:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:lm:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:lm:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:lm:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	10:18125244	17836291
Common		GRCh37			10	chr10	18125536	17836583	3	FN	T	C	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:ti:SNP:het:30	0/1:TP:gm:ti:SNP:het:30	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	10:18125536	17836583
Common		GRCh37			10	chr10	18125539	17836586	275	FN	C	T	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:ti:SNP:het:30	0/1:TP:gm:ti:SNP:het:30	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	10:18125539	17836586
Common		GRCh37			10	chr10	18125814	17836861	240	FN	A	T	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:tv:SNP:het:30	0/1:TP:gm:tv:SNP:het:30	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	10:18125814	17836861
Common		GRCh37			10	chr10	18126054	17837101	6	FN	T	G	GT:BD:BK:BI:BVT:BLT:QQ	1|1:TP:gm:tv:SNP:homalt:100	1/1:TP:gm:tv:SNP:homalt:100	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:tv:SNP:homalt:30	1/1:TP:gm:tv:SNP:homalt:30	1|1:TP:gm:tv:SNP:homalt:14.1	1/1:TP:gm:tv:SNP:homalt:14.1	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	10:18126054	17837101
Common		GRCh37			10	chr10	18126060	17837107	883	FN	G	A	GT:BD:BK:BI:BVT:BLT:QQ	1|1:TP:gm:ti:SNP:homalt:39.9993	1/1:TP:gm:ti:SNP:homalt:39.9993	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:ti:SNP:homalt:30	1/1:TP:gm:ti:SNP:homalt:30	1|1:TP:gm:ti:SNP:homalt:21.2	1/1:TP:gm:ti:SNP:homalt:21.2	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	10:18126060	17837107
NYGC	HG-002-2x250-b37.recalibrated.haplotypeCalls.vcf.gz	GRCh37	small-variants	SNP	10	chr10	18126943	17837990	0	FN	A	T	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0 	unsure	unsure	Although present in the HiFi Asm, it's not suppurted by ONT, PacBio, and Illumina	yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38																											10:18126943	17837990
Common		GRCh37			10	chr10	18126943	17837990	435	FN	A	T	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:tv:SNP:het:30	0/1:TP:gm:tv:SNP:het:30	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	10:18126943	17837990
Roche	RN_HG002_Illumina_PacBio_Oxford_GRCh37.vcf.gz	GRCh37	small-variants	SNP	10	chr10	18127378	17838425	131	FP_FN	G	A	GT:BD:BK:QQ:BI:BVT:BLT	0|1:FN:am:.:ti:SNP:het	1/1:FP:am:100:ti:SNP:homalt 	yes	no		yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38																											10:18127378	17838425
Common		GRCh37			10	chr10	18127509	17838556	686	FN	T	TA	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:i1_5:INDEL:het:30	0/1:TP:gm:i1_5:INDEL:het:30	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	10:18127509	17838556
Common		GRCh37			10	chr10	18128194	17839242	61	FN	C	G	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:tv:SNP:het:30	0/1:TP:gm:tv:SNP:het:30	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	10:18128194	17839242
Common		GRCh37			10	chr10	18128255	17839303	177	FN	C	A	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:tv:SNP:het:30	0/1:TP:gm:tv:SNP:het:30	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	10:18128255	17839303
Common		GRCh37			10	chr10	18128432	17839480	585	FN	C	CTTTAAAGAATTTGTGAAAATTCT	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:i16_plus:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|0:FN:.:i16_plus:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i16_plus:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:i16_plus:INDEL:het:30	0/1:TP:gm:i16_plus:INDEL:het:30	1|0:FN:.:i16_plus:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i16_plus:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i16_plus:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i16_plus:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	10:18128432	17839480
CMH_DRAGEN_3.6.3	NA24385.hard-filtered.vcf.gz	GRCh38	small-variants	INDEL	10	chr10	18128994	17840065	0	FP_FN	C	CA,CAA	GT:BD:BK:BI:QQ:BVT:BLT	1|2:FN:am:i1_5:.:INDEL:hetalt	1/1:FP:am:i1_5:90.03:INDEL:homalt	unsure	unsure	Conflicting evidences exist. Can't tell reliably that two polyA alleles differ by one in length.	yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38				yes	yes	homopolymer within SINE. ILMN read that cover homopolymer have no evidence of 2bp ins only 1bp and REF.  Hifi has extensive evidence of both variants across both HP. I'm putting SINE over homopolymer here, thinking Hifi likely accurate. ILMN reads with 2bp variant likely mapping to another location. 																						18128994
Common		GRCh38			10	chr10	18128994	17840065	230	FP_FN	C	CA,CAA	GT:BD:BK:BI:QQ:BVT:BLT	1|2:FN:am:i1_5:.:INDEL:hetalt	1/1:FP:am:i1_5:100:INDEL:homalt	CommonFP_FN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|2:FN:am:i1_5:.:INDEL:hetalt	1/1:FP:am:i1_5:230.73:INDEL:homalt	1|2:FN:am:i1_5:.:INDEL:hetalt	1/1:FP:am:i1_5:406.73:INDEL:homalt	1|2:FN:am:i1_5:.:INDEL:hetalt	1/1:FP:am:i1_5:30:INDEL:homalt	1|2:FN:am:i1_5:.:INDEL:hetalt	1/1:FP:am:i1_5:415.06:INDEL:homalt	1|2:FN:am:i1_5:.:INDEL:hetalt	1/1:FP:am:i1_5:0:INDEL:homalt	1|2:FN:am:i1_5:.:INDEL:hetalt	1/1:FP:am:i1_5:90.03:INDEL:homalt	1|2:FN:am:i1_5:.:INDEL:hetalt	1/1:FP:am:i1_5:9:INDEL:homalt		18128994
Common		GRCh37			10	chr10	18129224	17840295	568	FN	TA	T	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:d1_5:INDEL:het:30	0/1:TP:gm:d1_5:INDEL:het:30	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	10:18129224	17840295
Common		GRCh37			10	chr10	18129792	17840863	201	FN	C	T	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:ti:SNP:het:30	0/1:TP:gm:ti:SNP:het:30	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	10:18129792	17840863
Common		GRCh37			10	chr10	18129993	17841064	392	FN	G	A	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:ti:SNP:het:30	0/1:TP:gm:ti:SNP:het:30	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	10:18129993	17841064
Common		GRCh37			10	chr10	18130385	17841456	865	FN	A	G	GT:BD:BK:BI:BVT:BLT:QQ	1|1:TP:gm:ti:SNP:homalt:100	1/1:TP:gm:ti:SNP:homalt:100	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:ti:SNP:homalt:30	1/1:TP:gm:ti:SNP:homalt:30	1|1:TP:gm:ti:SNP:homalt:8.2	1/1:TP:gm:ti:SNP:homalt:8.2	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	10:18130385	17841456
Common		GRCh37			10	chr10	18131250	17842321	912	FN	A	G	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:ti:SNP:het:30	0/1:TP:gm:ti:SNP:het:30	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	10:18131250	17842321
Common		GRCh37			10	chr10	18132162	17843233	205	FN	G	T	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:lm:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:tv:SNP:het:30	0/1:TP:gm:tv:SNP:het:30	1|0:FN:lm:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:lm:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:lm:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	10:18132162	17843233
Common		GRCh37			10	chr10	18132367	17843438	472	FN	C	T	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:ti:SNP:het:30	0/1:TP:gm:ti:SNP:het:30	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	10:18132367	17843438
ITER	ITERteam_small-variation_GRCh37_ILMN-PB-ONT.vcf.gz	GRCh37	small-variants	SNP	10	chr10	18132839	17843910	0	FN	G	T	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	No	Yes	Few reads support this variant (only 2 reads for 10X and 3 for ONT, some of them with low MQ).	yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38																											10:18132839	17843910
Common		GRCh37			10	chr10	18132839	17843910	352	FN	G	T	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:tv:SNP:het:30	0/1:TP:gm:tv:SNP:het:30	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	10:18132839	17843910
Common		GRCh37			10	chr10	18133191	17844262	666	FN	C	A	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:tv:SNP:het:30	0/1:TP:gm:tv:SNP:het:30	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	10:18133191	17844262
Common		GRCh37			10	chr10	18133857	17844928	158	FN	G	A	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:ti:SNP:het:30	0/1:TP:gm:ti:SNP:het:30	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:lm:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	10:18133857	17844928
Common		GRCh37			10	chr10	18134015	17845086	681	FN	A	G	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:ti:SNP:het:30	0/1:TP:gm:ti:SNP:het:30	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	10:18134015	17845086
Common		GRCh37			10	chr10	18134696	17845767	425	FN	G	T	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:tv:SNP:het:30	0/1:TP:gm:tv:SNP:het:30	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	10:18134696	17845767
Common		GRCh37			10	chr10	18135121	17846192	150	FN	G	C	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:tv:SNP:het:30	0/1:TP:gm:tv:SNP:het:30	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	10:18135121	17846192
Common		GRCh37			10	chr10	18135271	17846342	367	FN	AT	A	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:d1_5:INDEL:het:30	0/1:TP:gm:d1_5:INDEL:het:30	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	10:18135271	17846342
Common		GRCh37			10	chr10	18135638	17846709	3	FN	C	T	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:ti:SNP:het:30	0/1:TP:gm:ti:SNP:het:30	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	10:18135638	17846709
Common		GRCh37			10	chr10	18135641	17846712	5	FN	C	T	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:ti:SNP:het:30	0/1:TP:gm:ti:SNP:het:30	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	10:18135641	17846712
Common		GRCh37			10	chr10	18135646	17846717	40	FN	C	T	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:ti:SNP:het:30	0/1:TP:gm:ti:SNP:het:30	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	10:18135646	17846717
Common		GRCh37			10	chr10	18135686	17846757	409	FP_FN	T	G	GT:BD:BK:QQ:BI:BVT:BLT	0|1:FN:am:.:tv:SNP:het	1/1:FP:am:100:tv:SNP:homalt	CommonFP_FN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													0|1:FN:.:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:am:.:tv:SNP:het	1/1:FP:am:691.77:tv:SNP:homalt	0|1:TP:gm:30:tv:SNP:het	0/1:TP:gm:30:tv:SNP:het	0|1:FN:am:.:tv:SNP:het	1/1:FP:am:781.03:tv:SNP:homalt	0|1:FN:am:.:tv:SNP:het	1/1:FP:am:0:tv:SNP:homalt	0|1:FN:am:.:tv:SNP:het	1/1:FP:am:47.75:tv:SNP:homalt	0|1:FN:am:.:tv:SNP:het	1/1:FP:am:35:tv:SNP:homalt	10:18135686	17846757
Common		GRCh37			10	chr10	18136095	17847166	301	FP_FN	T	C	GT:BD:BK:QQ:BI:BVT:BLT	0|1:FN:am:.:ti:SNP:het	1/1:FP:am:24.2022:ti:SNP:homalt	CommonFP_FN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													0|1:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:am:.:ti:SNP:het	1/1:FP:am:179.9:ti:SNP:homalt	0|1:TP:gm:30:ti:SNP:het	0/1:TP:gm:30:ti:SNP:het	0|1:FN:am:.:ti:SNP:het	1/1:FP:am:10.8:ti:SNP:homalt	0|1:FN:am:.:ti:SNP:het	1/1:FP:am:0:ti:SNP:homalt	0|1:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:am:.:ti:SNP:het	1/1:FP:am:35:ti:SNP:homalt	10:18136095	17847166
Common		GRCh37			10	chr10	18136396	17847467	131	FN	A	G	GT:BD:BK:BI:BVT:BLT:QQ	1|1:TP:gm:ti:SNP:homalt:100	1/1:TP:gm:ti:SNP:homalt:100	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:ti:SNP:homalt:30	1/1:TP:gm:ti:SNP:homalt:30	1|1:TP:gm:ti:SNP:homalt:30.8	1/1:TP:gm:ti:SNP:homalt:30.8	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	10:18136396	17847467
Common		GRCh37			10	chr10	18136527	17847598	8	FN	A	C	GT:BD:BK:BI:BVT:BLT:QQ	1|1:TP:gm:tv:SNP:homalt:100	1/1:TP:gm:tv:SNP:homalt:100	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:tv:SNP:homalt:30	1/1:TP:gm:tv:SNP:homalt:30	1|1:TP:gm:tv:SNP:homalt:12.9	1/1:TP:gm:tv:SNP:homalt:12.9	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	10:18136527	17847598
Common		GRCh37			10	chr10	18136535	17847606	184	FN	A	T	GT:BD:BK:BI:BVT:BLT:QQ	1|1:TP:gm:tv:SNP:homalt:100	1/1:TP:gm:tv:SNP:homalt:100	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:tv:SNP:homalt:30	1/1:TP:gm:tv:SNP:homalt:30	1|1:TP:gm:tv:SNP:homalt:19	1/1:TP:gm:tv:SNP:homalt:19	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	10:18136535	17847606
Common		GRCh37			10	chr10	18136719	17847790	31	FN	G	T	GT:BD:BK:BI:BVT:BLT:QQ	1|1:TP:gm:tv:SNP:homalt:100	1/1:TP:gm:tv:SNP:homalt:100	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:tv:SNP:homalt:30	1/1:TP:gm:tv:SNP:homalt:30	1|1:TP:gm:tv:SNP:homalt:26.7	1/1:TP:gm:tv:SNP:homalt:26.7	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	10:18136719	17847790
Common		GRCh37			10	chr10	18136750	17847821	877	FN	A	ACT	GT:BD:BK:BI:BVT:BLT:QQ	1|1:TP:gm:i1_5:INDEL:homalt:33.0106	1/1:TP:gm:i1_5:INDEL:homalt:33.0106	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:i1_5:INDEL:homalt:30	1/1:TP:gm:i1_5:INDEL:homalt:30	1|1:TP:gm:i1_5:INDEL:homalt:23.4	1/1:TP:gm:i1_5:INDEL:homalt:23.4	1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	10:18136750	17847821
Common		GRCh37			10	chr10	18137627	17848698	150	FN	C	T	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:ti:SNP:homalt:30	1/1:TP:gm:ti:SNP:homalt:30	1|1:TP:gm:ti:SNP:homalt:20.7	1/1:TP:gm:ti:SNP:homalt:20.7	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	10:18137627	17848698
Common		GRCh37			10	chr10	18137777	17848848	455	FN	A	G	GT:BD:BK:BI:BVT:BLT:QQ	1|1:TP:gm:ti:SNP:homalt:100	1/1:TP:gm:ti:SNP:homalt:100	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:ti:SNP:homalt:30	1/1:TP:gm:ti:SNP:homalt:30	1|1:TP:gm:ti:SNP:homalt:27.1	1/1:TP:gm:ti:SNP:homalt:27.1	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	10:18137777	17848848
Common		GRCh37			10	chr10	18138232	17849303	154	FN	T	TA	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:lm:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:i1_5:INDEL:homalt:30	1/1:TP:gm:i1_5:INDEL:homalt:30	1|1:FN:lm:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	10:18138232	17849303
Common		GRCh37			10	chr10	18138386	17849457	101	FN	G	A	GT:BD:BK:BI:BVT:BLT:QQ	1|1:TP:gm:ti:SNP:homalt:17.2101	1/1:TP:gm:ti:SNP:homalt:17.2101	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:ti:SNP:homalt:30	1/1:TP:gm:ti:SNP:homalt:30	1|1:TP:gm:ti:SNP:homalt:18.9	1/1:TP:gm:ti:SNP:homalt:18.9	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	10:18138386	17849457
Roche	RN_HG002_Illumina_PacBio_Oxford_GRCh37.vcf.gz	GRCh37	small-variants	SNP	10	chr10	18138487	17849558	0	FN	G	A	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0 	yes	no	the reason not detected by us: missed in Illumina/PacBio (only in ONT/10x, low-cov in PB) not even in candids	yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38																											10:18138487	17849558
Common		GRCh37			10	chr10	18138487	17849558	1	FN	G	A	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:ti:SNP:homalt:30	1/1:TP:gm:ti:SNP:homalt:30	1|1:TP:gm:ti:SNP:homalt:14.4	1/1:TP:gm:ti:SNP:homalt:14.4	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	10:18138487	17849558
Common		GRCh37			10	chr10	18138488	17849559	142	FN	A	AC	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:i1_5:INDEL:homalt:30	1/1:TP:gm:i1_5:INDEL:homalt:30	1|1:FN:lm:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	10:18138488	17849559
Common		GRCh37			10	chr10	18138630	17849701	9	FN	G	A	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:ti:SNP:het:30	0/1:TP:gm:ti:SNP:het:30	1|0:FN:lm:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	10:18138630	17849701
PacBio_gatk4	gatk4hc_HG002_15kb_20kb_52X_SequelII.vcf.gz	GRCh37	small-variants	SNP	10	chr10	18138639	17849710	0	FN	A	G	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	yes	no		yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38																											10:18138639	17849710
Common		GRCh37			10	chr10	18138639	17849710	17	FN	A	G	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:lm:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:ti:SNP:homalt:30	1/1:TP:gm:ti:SNP:homalt:30	1|1:TP:gm:ti:SNP:homalt:5.9	1/1:TP:gm:ti:SNP:homalt:5.9	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	10:18138639	17849710
Common		GRCh37			10	chr10	18138656	17849727	9	FN	C	T	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:lm:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:ti:SNP:homalt:30	1/1:TP:gm:ti:SNP:homalt:30	1|1:TP:gm:ti:SNP:homalt:12.4	1/1:TP:gm:ti:SNP:homalt:12.4	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	10:18138656	17849727
Common		GRCh37			10	chr10	18138665	17849736	82	FN	G	C	GT:BD:BK:BI:BVT:BLT:QQ	1|1:TP:gm:tv:SNP:homalt:100	1/1:TP:gm:tv:SNP:homalt:100	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:tv:SNP:homalt:30	1/1:TP:gm:tv:SNP:homalt:30	1|1:TP:gm:tv:SNP:homalt:16.6	1/1:TP:gm:tv:SNP:homalt:16.6	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	10:18138665	17849736
Common		GRCh37			10	chr10	18138747	17849818	371	FN	T	C	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:ti:SNP:homalt:30	1/1:TP:gm:ti:SNP:homalt:30	1|1:TP:gm:ti:SNP:homalt:20.8	1/1:TP:gm:ti:SNP:homalt:20.8	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	10:18138747	17849818
Common		GRCh37			10	chr10	18139118	17850189	67	FN	T	C	GT:BD:BK:BI:BVT:BLT:QQ	0|1:TP:gm:ti:SNP:het:100	0/1:TP:gm:ti:SNP:het:100	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:TP:gm:ti:SNP:het:30	0/1:TP:gm:ti:SNP:het:30	0|1:TP:gm:ti:SNP:het:5	0/1:TP:gm:ti:SNP:het:5	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	10:18139118	17850189
NYGC	HG-002-2x250-b37.recalibrated.haplotypeCalls.vcf.gz	GRCh37	small-variants	INDEL	10	chr10	18139185	17850256	0	FN	G	GTTTTT,GTTTTTTTT	GT:BD:BK:BI:BVT:BLT:QQ	1|2:FN:.:i1_5,i6_15:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:0 	yes	no		yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38																											10:18139185	17850256
Common		GRCh37			10	chr10	18139185	17850256	809	FN	G	GTTTTT,GTTTTTTTT	GT:BD:BK:BI:BVT:BLT:QQ	1|2:FN:.:i1_5,i6_15:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|2:FN:.:i1_5,i6_15:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:0	1|2:FN:.:i1_5,i6_15:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:0	1|2:TP:gm:i1_5,i6_15:INDEL:hetalt:30	2/1:TP:gm:i1_5,i6_15:INDEL:hetalt:30	1|2:FN:.:i1_5,i6_15:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:0	1|2:FN:.:i1_5,i6_15:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:0	1|2:FN:.:i1_5,i6_15:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:0	1|2:FN:.:i1_5,i6_15:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:0	10:18139185	17850256
Roche	RN_HG002_Illumina_PacBio_Oxford_GRCh37.vcf.gz	GRCh37	small-variants	SNP	10	chr10	18139994	17851065	0	FN	A	G	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0 	yes	no	the reason not detected by us: missed in Illumina/PacBio (only in 10x) not even in candids	yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38																											10:18139994	17851065
Common		GRCh37			10	chr10	18139994	17851065	135	FN	A	G	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:ti:SNP:het:30	0/1:TP:gm:ti:SNP:het:30	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	10:18139994	17851065
Common		GRCh37			10	chr10	18140129	17851200	180	FN	A	G	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:ti:SNP:het:30	0/1:TP:gm:ti:SNP:het:30	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:lm:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	10:18140129	17851200
Common		GRCh37			10	chr10	18140309	17851380	299	FN	A	T	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:lm:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:lm:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:tv:SNP:het:30	0/1:TP:gm:tv:SNP:het:30	1|0:FN:lm:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:lm:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:lm:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	10:18140309	17851380
Common		GRCh37			10	chr10	18140608	17851679	726	FN	T	G	GT:BD:BK:BI:BVT:BLT:QQ	1|1:TP:gm:tv:SNP:homalt:100	1/1:TP:gm:tv:SNP:homalt:100	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:tv:SNP:homalt:30	1/1:TP:gm:tv:SNP:homalt:30	1|1:TP:gm:tv:SNP:homalt:27.7	1/1:TP:gm:tv:SNP:homalt:27.7	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	10:18140608	17851679
CMH_DRAGEN_3.6.3	NA24385.hard-filtered.vcf.gz	GRCh37	small-variants	SNP	10	chr10	18141334	17852405	1283	FN	T	G	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	unsure	no	In seg dup. Some including 10X and Nanopore show the variant. However, allele fraction is constantly and significantly skewed (~7:3) in all the datasets.  No evidence in PacBio and mapping quality of Nanopore is not good.	yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38																											10:18141334	17852405
Common		GRCh37			10	chr10	18142617	17853688	264	FN	G	A	GT:BD:BK:BI:BVT:BLT:QQ	1|1:TP:gm:ti:SNP:homalt:100	1/1:TP:gm:ti:SNP:homalt:100	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:ti:SNP:homalt:30	1/1:TP:gm:ti:SNP:homalt:30	1|1:TP:gm:ti:SNP:homalt:23.4	1/1:TP:gm:ti:SNP:homalt:23.4	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	10:18142617	17853688
Roche	RN_HG002_Illumina_PacBio_Oxford_GRCh37.vcf.gz	GRCh37	small-variants	SNP	10	chr10	18142881	17853952	0	FN	T	G	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0 	yes	no	the reason not detected by us: missed in Illumina/PacBio (only in ONT/10x, low-cov in PB) not even in candids	yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38																											10:18142881	17853952
Common		GRCh37			10	chr10	18142881	17853952	237	FN	T	G	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:tv:SNP:homalt:30	1/1:TP:gm:tv:SNP:homalt:30	1|1:TP:gm:tv:SNP:homalt:28.9	1/1:TP:gm:tv:SNP:homalt:28.9	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	10:18142881	17853952
NYGC	HG-002-2x250-b37.recalibrated.haplotypeCalls.vcf.gz	GRCh37	small-variants	SNP	10	chr10	18143118	17854189	1275	FN	C	T	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0 	yes	no		yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38																											10:18143118	17854189
Common		GRCh37			10	chr10	18144393	17855464	669	FN	A	G	GT:BD:BK:BI:BVT:BLT:QQ	1|1:TP:gm:ti:SNP:homalt:33.0111	1/1:TP:gm:ti:SNP:homalt:33.0111	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:ti:SNP:homalt:30	1/1:TP:gm:ti:SNP:homalt:30	1|1:TP:gm:ti:SNP:homalt:35.2	1/1:TP:gm:ti:SNP:homalt:35.2	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	10:18144393	17855464
Common		GRCh37			10	chr10	18145062	17856133	88	FN	G	T	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:tv:SNP:het:30	0/1:TP:gm:tv:SNP:het:30	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	10:18145062	17856133
Common		GRCh37			10	chr10	18145150	17856221	1801	FN	C	T	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:ti:SNP:het:30	0/1:TP:gm:ti:SNP:het:30	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:lm:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	10:18145150	17856221
Common		GRCh37			10	chr10	18146951	17858022	912	FN	G	A	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:ti:SNP:het:30	0/1:TP:gm:ti:SNP:het:30	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	10:18146951	17858022
Common		GRCh37			10	chr10	18147863	17858934	262	FN	C	T	GT:BD:BK:BI:BVT:BLT:QQ	0|1:TP:gm:ti:SNP:het:100	0/1:TP:gm:ti:SNP:het:100	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:TP:gm:ti:SNP:het:30	0/1:TP:gm:ti:SNP:het:30	0|1:TP:gm:ti:SNP:het:17.9	0/1:TP:gm:ti:SNP:het:17.9	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	10:18147863	17858934
Common		GRCh37			10	chr10	18148125	17859196	512	FN	T	C	GT:BD:BK:BI:BVT:BLT:QQ	1|0:TP:gm:ti:SNP:het:14.4408	0/1:TP:gm:ti:SNP:het:14.4408	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:ti:SNP:het:30	0/1:TP:gm:ti:SNP:het:30	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	10:18148125	17859196
Common		GRCh37			10	chr10	18148637	17859708	73	FN	G	A	GT:BD:BK:BI:BVT:BLT:QQ	0|1:TP:gm:ti:SNP:het:100	0/1:TP:gm:ti:SNP:het:100	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:TP:gm:ti:SNP:het:30	0/1:TP:gm:ti:SNP:het:30	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	10:18148637	17859708
Common		GRCh37			10	chr10	18148710	17859781	11	FN	G	A	GT:BD:BK:BI:BVT:BLT:QQ	0|1:TP:gm:ti:SNP:het:100	0/1:TP:gm:ti:SNP:het:100	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:TP:gm:ti:SNP:het:30	0/1:TP:gm:ti:SNP:het:30	0|1:TP:gm:ti:SNP:het:11.1	0/1:TP:gm:ti:SNP:het:11.1	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	10:18148710	17859781
Common		GRCh37			10	chr10	18148721	17859792	355	FN	T	C	GT:BD:BK:BI:BVT:BLT:QQ	0|1:TP:gm:ti:SNP:het:100	0/1:TP:gm:ti:SNP:het:100	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:TP:gm:ti:SNP:het:30	0/1:TP:gm:ti:SNP:het:30	0|1:TP:gm:ti:SNP:het:13.4	0/1:TP:gm:ti:SNP:het:13.4	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	10:18148721	17859792
PacBio_gatk4	gatk4hc_HG002_15kb_20kb_52X_SequelII.vcf.gz	GRCh37	small-variants	SNP	10	chr10	18149076	17860147	420	FN	A	G	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	yes	no		yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38																											10:18149076	17860147
Common		GRCh37			10	chr10	18149496	17860567	1110	FN	T	G	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:tv:SNP:het:30	0/1:TP:gm:tv:SNP:het:30	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	10:18149496	17860567
Common		GRCh37			10	chr10	18150606	17861677	545	FN	C	T	GT:BD:BK:BI:BVT:BLT:QQ	0|1:TP:gm:ti:SNP:het:100	0/1:TP:gm:ti:SNP:het:100	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:TP:gm:ti:SNP:het:30	0/1:TP:gm:ti:SNP:het:30	0|1:TP:gm:ti:SNP:het:14.9	0/1:TP:gm:ti:SNP:het:14.9	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	10:18150606	17861677
Common		GRCh37			10	chr10	18151151	17862222	631	FN	TA	T	GT:BD:BK:BI:BVT:BLT:QQ	0|1:TP:gm:d1_5:INDEL:het:100	0/1:TP:gm:d1_5:INDEL:het:100	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:TP:gm:d1_5:INDEL:het:30	0/1:TP:gm:d1_5:INDEL:het:30	0|1:TP:gm:d1_5:INDEL:het:5.9	0/1:TP:gm:d1_5:INDEL:het:5.9	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	10:18151151	17862222
Common		GRCh37			10	chr10	18151782	17862853	245	FN	A	G	GT:BD:BK:BI:BVT:BLT:QQ	1|1:TP:gm:ti:SNP:homalt:100	1/1:TP:gm:ti:SNP:homalt:100	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:ti:SNP:homalt:30	1/1:TP:gm:ti:SNP:homalt:30	1|1:TP:gm:ti:SNP:homalt:11	1/1:TP:gm:ti:SNP:homalt:11	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	10:18151782	17862853
Common		GRCh37			10	chr10	18152027	17863098	588	FN	C	T	GT:BD:BK:BI:BVT:BLT:QQ	0|1:TP:gm:ti:SNP:het:100	0/1:TP:gm:ti:SNP:het:100	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:TP:gm:ti:SNP:het:30	0/1:TP:gm:ti:SNP:het:30	0|1:TP:gm:ti:SNP:het:11.7	0/1:TP:gm:ti:SNP:het:11.7	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	10:18152027	17863098
Common		GRCh37			10	chr10	18152615	17863686	811	FN	C	T	GT:BD:BK:BI:BVT:BLT:QQ	1|1:TP:gm:ti:SNP:homalt:30.97	1/1:TP:gm:ti:SNP:homalt:30.97	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:ti:SNP:homalt:30	1/1:TP:gm:ti:SNP:homalt:30	1|1:TP:gm:ti:SNP:homalt:14.3	1/1:TP:gm:ti:SNP:homalt:14.3	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	10:18152615	17863686
Common		GRCh37			10	chr10	18153426	17864497	674	FN	A	G	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:ti:SNP:het:30	0/1:TP:gm:ti:SNP:het:30	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	10:18153426	17864497
NYGC	HG-002-2x250-b37.recalibrated.haplotypeCalls.vcf.gz	GRCh37	small-variants	SNP	10	chr10	18154100	17865171	43	FP_FN	G	A	GT:BD:BK:QQ:BI:BVT:BLT	0|1:FN:am:.:ti:SNP:het	1/1:FP:am:196.78:ti:SNP:homalt 	yes	yes		yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38																											10:18154100	17865171
Common		GRCh37			10	chr10	18154143	17865214	1124	FN	A	G	GT:BD:BK:BI:BVT:BLT:QQ	1|0:TP:gm:ti:SNP:het:18.9052	0/1:TP:gm:ti:SNP:het:18.9052	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:ti:SNP:het:30	0/1:TP:gm:ti:SNP:het:30	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	10:18154143	17865214
Common		GRCh37			10	chr10	18155267	17866338	24	FN	G	A	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:lm:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:lm:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:ti:SNP:het:30	0/1:TP:gm:ti:SNP:het:30	1|0:FN:lm:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:lm:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:lm:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:lm:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	10:18155267	17866338
Common		GRCh37			10	chr10	18155291	17866362	116	FN	T	C	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:lm:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:lm:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:ti:SNP:het:30	0/1:TP:gm:ti:SNP:het:30	1|0:FN:lm:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:lm:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:lm:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:lm:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	10:18155291	17866362
Common		GRCh37			10	chr10	18155407	17866478	886	FN	C	G	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:tv:SNP:het:30	0/1:TP:gm:tv:SNP:het:30	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	10:18155407	17866478
Common		GRCh37			10	chr10	18156293	17867364	8836719	FN	C	CCTT	GT:BD:BK:BI:BVT:BLT:QQ	0|1:TP:gm:i1_5:INDEL:het:32.2185	0/1:TP:gm:i1_5:INDEL:het:32.2185	CommonFN			yes	no	GRCh37 has false duplication of MRC1 corrected in GRCh38													0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:TP:gm:i1_5:INDEL:het:30	0/1:TP:gm:i1_5:INDEL:het:30	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	10:18156293	17867364
Roche	RN_HG002_Illumina_PacBio_Oxford_GRCh37.vcf.gz	GRCh37	small-variants	INDEL	10	chr10	26993012	26704083	36058	FP_FN	C	CAAAAAAAAAAAAAAAA,CAAAAAAAAAAAAAAAAAAAAAAAA	GT:BD:BK:BI:QQ:BVT:BLT	1|2:FN:am:i16_plus:.:INDEL:hetalt	0/1:FP:am:i16_plus:100:INDEL:het 	yes	no																															10:26993012	26704083
NCBI	HG002_grch38_dipcall.vcf.gz	GRCh38	small-variants	INDEL	10	chr10	27029070	26740141	60959510	FP_FN	C	CA	GT:BD:BK:QQ:BI:BVT:BLT	1|0:FN:am:.:i1_5:INDEL:het	1/1:FP:am:30:i1_5:INDEL:homalt	yes	no	evidence for HET							skip																								27029070
PacBio_gatk4	gatk4hc_HG002_15kb_20kb_52X_SequelII.vcf.gz	GRCh37	small-variants	INDEL	10	chr10	89459408	87699651	0	FN	ACCAT	A	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	no	yes	no read support	no	yes	likely consensus error in hifiasm since not supported																											10:89459408	87699651
Common		GRCh37			10	chr10	89459408	87699651	0	FN	ACCAT	A	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no	yes	likely consensus error in hifiasm since not supported													0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	10:89459408	87699651
Common		GRCh38			10	chr10	89459408	87699651	161	FN	ACCAT	A	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no	yes	likely consensus error in hifiasm since not supported													0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0		89459408
DNAnexus	GRCh38_HG002_WGS_union.vcf.gz	GRCh38	small-variants	INDEL	10	chr10	89459569	87699812	34851	FN	T	TA	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0 	yes	no	The variant is called by 3 of 4 short-read variant callers. It didn't get included in the VCF because the variant representation formatting issue.	yes	no					skip																								89459569
Common		GRCh37			10	chr10	89494420	87734663	0	FP_FN	GTATATA	G	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:d6_15:INDEL:homalt	0/1:FP:am:100:d6_15:INDEL:het	CommonFP_FN			no		not sure why benchmark misses ins on other haplotype since there are nearby hets													1|1:FN:lm:.:d6_15:INDEL:homalt	.:.:.:0:.:NOCALL:nocall	1|1:TP:gm:460.73:d6_15:INDEL:homalt	1/1:TP:gm:460.73:d6_15:INDEL:homalt	1|1:FN:am:.:d6_15:INDEL:homalt	0/1:FP:am:30:d6_15:INDEL:het	1|1:FN:am:.:d6_15:INDEL:homalt	0/1:FP:am:888.06:d6_15:INDEL:het	1|1:FN:am:.:d6_15:INDEL:homalt	0/1:FP:am:0:d6_15:INDEL:het	1|1:FN:am:.:d6_15:INDEL:homalt	0/1:FP:am:116.38:d6_15:INDEL:het	1|1:FN:am:.:d6_15:INDEL:homalt	0/1:FP:am:9:d6_15:INDEL:het	10:89494420	87734663
Common		GRCh38			10	chr10	89494420	87734663	6	FP_FN	GTATATA	G	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:d6_15:INDEL:homalt	0/1:FP:am:100:d6_15:INDEL:het	CommonFP_FN			no		not sure why benchmark misses ins on other haplotype since there are nearby hets													1|1:FN:lm:.:d6_15:INDEL:homalt	.:.:.:0:.:NOCALL:nocall	1|1:TP:gm:320.73:d6_15:INDEL:homalt	1/1:TP:gm:320.73:d6_15:INDEL:homalt	1|1:FN:am:.:d6_15:INDEL:homalt	0/1:FP:am:30:d6_15:INDEL:het	1|1:TP:gm:288.98:d6_15:INDEL:homalt	1/1:TP:gm:288.98:d6_15:INDEL:homalt	1|1:FN:am:.:d6_15:INDEL:homalt	0/1:FP:am:0:d6_15:INDEL:het	1|1:FN:am:.:d6_15:INDEL:homalt	0/1:FP:am:119.2:d6_15:INDEL:het	1|1:FN:am:.:d6_15:INDEL:homalt	0/1:FP:am:9:d6_15:INDEL:het		89494420
Common		GRCh37			10	chr10	89494426	87734669	142250	FP	A	ATATATA,ATATA	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/2:100:FP:lm:i1_5:INDEL:het	CommonFP			no		not sure why benchmark misses ins on other haplotype since there are nearby hets													./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/2:30:FP:lm:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/2:888.06:FP:lm:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/2:0:FP:lm:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:116.38:FP:lm:i6_15:INDEL:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	10:89494426	87734669
Common		GRCh37			10	chr10	89636676	87876919	0	FP_FN	C	CT	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:am:i1_5:INDEL:homalt:.	0/1:FP:am:i1_5:INDEL:het:100	CommonFP_FN			no		likely error due to noisy hifi reads in homopolymer													1|1:FN:am:i1_5:INDEL:homalt:.	0/1:FP:am:i1_5:INDEL:het:33	1|1:FN:am:i1_5:INDEL:homalt:.	0/1:FP:am:i1_5:INDEL:het:155.73	1|1:FN:am:i1_5:INDEL:homalt:.	0/1:FP:am:i1_5:INDEL:het:30	1|1:FN:am:i1_5:INDEL:homalt:.	0/1:FP:am:i1_5:INDEL:het:143.64	1|1:FN:am:i1_5:INDEL:homalt:.	0/1:FP:am:i1_5:INDEL:het:0	1|1:FN:am:i1_5:INDEL:homalt:.	0/1:FP:am:i1_5:INDEL:het:50	1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	10:89636676	87876919
Common		GRCh38			10	chr10	89636676	87876919	13508699	FP_FN	C	CT	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:100:i1_5:INDEL:het	CommonFP_FN			no		likely error due to noisy hifi reads in homopolymer													1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:33:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:123.73:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:30:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:76.64:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:0:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:50:i1_5:INDEL:het	1|1:FN:.:.:i1_5:INDEL:homalt	.:.:.:0:.:NOCALL:nocall		89636676
Common		GRCh37			10	chr10	103145375	101385618	1910	FP_FN	C	CTTTTTTTTT,CTTTTTTTTTT	GT:BD:BK:BI:QQ:BVT:BLT	2|1:FN:am:i6_15:.:INDEL:hetalt	1/1:FP:am:i6_15:100:INDEL:homalt	CommonFP_FN			unsure	unsure	all techs noisy in long ins in homopolymer in low complexity region													2|1:FN:.:i6_15:.:INDEL:hetalt	.:.:.:.:0:NOCALL:nocall	2|1:FN:am:i6_15:.:INDEL:hetalt	1/1:FP:am:i6_15:356.73:INDEL:homalt	2|1:FN:am:i6_15:.:INDEL:hetalt	2/2:FP:am:i6_15:30:INDEL:homalt	2|1:FN:am:i6_15:.:INDEL:hetalt	0/1:FP:am:i6_15:178.62:INDEL:het	2|1:FN:lm:i6_15:.:INDEL:hetalt	.:.:.:.:0:NOCALL:nocall	2|1:FN:.:i6_15:.:INDEL:hetalt	.:.:.:.:0:NOCALL:nocall	2|1:FN:am:i6_15:.:INDEL:hetalt	1/1:FP:am:i6_15:13:INDEL:homalt	10:103145375	101385618
Common		GRCh37			10	chr10	103147285	101387528	0	FP_FN	CTT	C,CTTTTTTTTTTTTTTT	GT:BD:BK:BI:QQ:BVT:BLT	2|1:TP:gm:d1_5,i6_15:100:INDEL:hetalt	0/1:TP:gm:d1_5:100:INDEL:het	CommonFP_FN			yes		benchmark likely correct despite large insertion in long homopolymer, since it's supported by illumina and HiFi													2|1:TP:gm:d1_5,i6_15:1860.73:INDEL:hetalt	0/1:TP:gm:d1_5:1860.73:INDEL:het	2|1:FN:am:d1_5,i6_15:.:INDEL:hetalt	1/1:FP:am:d1_5:753.73:INDEL:homalt	2|1:FN:am:d1_5,i6_15:.:INDEL:hetalt	1/1:FP:am:d1_5:30:INDEL:homalt	2|1:FN:am:d1_5,i6_15:.:INDEL:hetalt	1/1:FP:am:d1_5:564.1:INDEL:homalt	2|1:FN:.:d1_5,i6_15:.:INDEL:hetalt	.:.:.:.:0:NOCALL:nocall	2|1:FN:am:d1_5,i6_15:.:INDEL:hetalt	1/1:FP:am:d1_5:62.31:INDEL:homalt	2|1:FN:am:d1_5,i6_15:.:INDEL:hetalt	0/1:FP:am:d1_5:13:INDEL:het	10:103147285	101387528
Common		GRCh38			10	chr10	103147285	101387528	16497	FP_FN	CTT	C,CTTTTTTTTTTTTTTT	GT:BD:BK:QQ:BI:BVT:BLT	2|1:TP:gm:100:d1_5,i6_15:INDEL:hetalt	0/1:TP:gm:100:d1_5:INDEL:het	CommonFP_FN			yes		benchmark likely correct despite large insertion in long homopolymer, since it's supported by illumina and HiFi													2|1:TP:gm:1860.73:d1_5,i6_15:INDEL:hetalt	0/1:TP:gm:1860.73:d1_5:INDEL:het	2|1:FN:am:.:d1_5,i6_15:INDEL:hetalt	1/1:FP:am:753.73:d1_5:INDEL:homalt	2|1:FN:am:.:d1_5,i6_15:INDEL:hetalt	1/1:FP:am:30:d1_5:INDEL:homalt	2|1:FN:am:.:d1_5,i6_15:INDEL:hetalt	1/1:FP:am:340.1:d1_5:INDEL:homalt	2|1:FN:.:.:d1_5,i6_15:INDEL:hetalt	.:.:.:0:.:NOCALL:nocall	2|1:FN:am:.:d1_5,i6_15:INDEL:hetalt	1/1:FP:am:62.31:d1_5:INDEL:homalt	2|1:FN:am:.:d1_5,i6_15:INDEL:hetalt	1/1:FP:am:14:d1_5:INDEL:homalt		103147285
Common		GRCh37			10	chr10	103163782	101404025	21601	FN	TA	T	GT:BD:BK:BI:BVT:BLT:QQ	1|0:TP:gm:d1_5:INDEL:het:26.1979	0/1:TP:gm:d1_5:INDEL:het:26.1979	CommonFN			yes	no	illumina supports very complex variant in adjacent diTRs and homopolymer													1|0:FN:lm:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:lm:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:lm:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:lm:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:d1_5:INDEL:het:0	0/1:TP:gm:d1_5:INDEL:het:0	1|0:TP:gm:d1_5:INDEL:het:50	0/1:TP:gm:d1_5:INDEL:het:50	1|0:FN:lm:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	10:103163782	101404025
Common		GRCh37			10	chr10	103185383	101425626	0	FP_FN	CT	C	GT:BD:BK:QQ:BI:BVT:BLT	0|1:FN:am:.:d1_5:INDEL:het	1/1:FP:am:100:d1_5:INDEL:homalt	CommonFP_FN			no	yes	benchmark error likely due to noise in HiFi in homopolymer													0|1:TP:gm:617.19:d1_5:INDEL:het	0/1:TP:gm:617.19:d1_5:INDEL:het	0|1:FN:am:.:d1_5:INDEL:het	1/1:FP:am:1139.73:d1_5:INDEL:homalt	0|1:FN:am:.:d1_5:INDEL:het	1/1:FP:am:30:d1_5:INDEL:homalt	0|1:TP:gm:689.75:d1_5:INDEL:het	0/1:TP:gm:689.75:d1_5:INDEL:het	0|1:FN:am:.:d1_5:INDEL:het	1/1:FP:am:0:d1_5:INDEL:homalt	0|1:FN:am:.:d1_5:INDEL:het	1/1:FP:am:119.96:d1_5:INDEL:homalt	0|1:FN:am:.:d1_5:INDEL:het	1/1:FP:am:9:d1_5:INDEL:homalt	10:103185383	101425626
Common		GRCh38			10	chr10	103185383	101425626	3878	FP_FN	CT	C	GT:BD:BK:QQ:BI:BVT:BLT	0|1:FN:am:.:d1_5:INDEL:het	1/1:FP:am:100:d1_5:INDEL:homalt	CommonFP_FN			no	yes	benchmark error likely due to noise in HiFi in homopolymer													0|1:TP:gm:617.19:d1_5:INDEL:het	0/1:TP:gm:617.19:d1_5:INDEL:het	0|1:FN:am:.:d1_5:INDEL:het	1/1:FP:am:1188.73:d1_5:INDEL:homalt	0|1:FN:am:.:d1_5:INDEL:het	1/1:FP:am:30:d1_5:INDEL:homalt	0|1:FN:am:.:d1_5:INDEL:het	1/1:FP:am:517.03:d1_5:INDEL:homalt	0|1:FN:am:.:d1_5:INDEL:het	1/1:FP:am:0:d1_5:INDEL:homalt	0|1:FN:am:.:d1_5:INDEL:het	1/1:FP:am:119.96:d1_5:INDEL:homalt	0|1:FN:am:.:d1_5:INDEL:het	1/1:FP:am:9:d1_5:INDEL:homalt		103185383
Common		GRCh37			10	chr10	103189261	101429504	18418	FP_FN	T	TC,TCC	GT:BD:BK:BI:QQ:BVT:BLT	2|1:FN:am:i1_5:.:INDEL:hetalt	1/1:FP:am:i1_5:100:INDEL:homalt	CommonFP_FN			no	yes	benchmark likely gets C homopolymer length wrong on one haplotype due to noise													2|1:FN:lm:i1_5:.:INDEL:hetalt	.:.:.:.:0:NOCALL:nocall	2|1:FN:am:i1_5:.:INDEL:hetalt	1/1:FP:am:i1_5:206.75:INDEL:homalt	2|1:FN:am:i1_5:.:INDEL:hetalt	1/1:FP:am:i1_5:30:INDEL:homalt	2|1:FN:lm:i1_5:.:INDEL:hetalt	.:.:.:.:0:NOCALL:nocall	2|1:FN:am:i1_5:.:INDEL:hetalt	1/1:FP:am:i1_5:0:INDEL:homalt	2|1:FN:am:i1_5:.:INDEL:hetalt	1/1:FP:am:i1_5:65.12:INDEL:homalt	2|1:FN:am:i1_5:.:INDEL:hetalt	1/1:FP:am:i1_5:3:INDEL:homalt	10:103189261	101429504
PacBio_gatk4	gatk4hc_HG002_15kb_20kb_52X_SequelII.vcf.gz	GRCh37	small-variants	INDEL	10	chr10	103207679	101447922	28000	FP	C	CA	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:317.73:FP:.:i1_5:INDEL:het	yes	no	indel doesn't segregate with phase																														10:103207679	101447922
BCM-HGSC_xAtlas	HG002.hs37d5.60x.1_merged.vcf.gz	GRCh37	small-variants	INDEL	10	chr10	103235679	101475922	6471	FP	C	CATATATATATAT	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	1/1:12:FP:am:i6_15:INDEL:homalt 	Yes	No																															10:103235679	101475922
Common		GRCh37			10	chr10	103242150	101482393	0	FN	C	CT	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			unsure	unsure	all techs are noisy in long A homopolymer													0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	10:103242150	101482393
BCM-HGSC_xAtlas	HG002.GRCh38.60x.1_merged.vcf.gz	GRCh38	small-variants	INDEL	10	chr10	103242150	101482393	0	FN	C	CT	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0 	Yes	No		unsure	unsure	all techs are noisy in long A homopolymer				skip																								103242150
Common		GRCh38			10	chr10	103242150	101482393	50392	FN	C	CT	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			unsure	unsure	all techs are noisy in long A homopolymer													0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0		103242150
Roche	RN_HG002_Illumina_PacBio_Oxford_GRCh37.vcf.gz	GRCh37	small-variants	SNP	10	chr10	103292542	101532785	31830594	FP	T	C	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:am:ti:SNP:het 	yes	no																															10:103292542	101532785
DNAnexus	hs37d5_HG002_WGS_union.vcf.gz	GRCh37	small-variants	SNP	10	chr10	135176883	133363379	58996	FP_FN	A	G	GT:BD:BK:QQ:BI:BVT:BLT	1|0:FN:am:.:ti:SNP:het	1/1:FP:am:0:ti:SNP:homalt	unsure	unsure	I will suggest call this region as an insertion variant, rather than SNP. This region is complicated. The position is only 2 base pair away from a insertion variant, according to all sequencing technology sources. Also, this region is heavily  CA repeat. 	yes	no	benchmark supported by illumina in complex diTR variant																											10:135176883	133363379
Common		GRCh37			10	chr10	135235879	133422375	0	FN	TTGGCAGTTGCTGTGCCCTGAGAACAGGCAGAACTGTGTGA	T	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:lm:d16_plus:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no	yes	40bp del is likely a hifiasm consensus error since only supported by one read - nearby 51bp ins from same read already excluded													0|1:FN:lm:d16_plus:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:d16_plus:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:d16_plus:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:d16_plus:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:d16_plus:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:d16_plus:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:d16_plus:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	10:135235879	133422375
Common		GRCh38			10	chr10	135235879	133422375	11	FN	TTGGCAGTTGCTGTGCCCTGAGAACAGGCAGAACTGTGTGA	T	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:lm:d16_plus:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no	yes	40bp del is likely a hifiasm consensus error since only supported by one read - nearby 51bp ins from same read already excluded													0|1:FN:lm:d16_plus:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:d16_plus:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:d16_plus:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:d16_plus:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:d16_plus:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:d16_plus:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:d16_plus:INDEL:het:.	.:.:.:.:NOCALL:nocall:0		135235879
Common		GRCh37			10	chr10	135235890	133422386	0	FP_FN	T	C,*	GT:BD:BK:BI:QQ:BVT:BLT	1|2:FN:am:ti:.:SNP:hetalt	1/1:FP:am:ti:100:SNP:homalt	CommonFP_FN			no	yes	40bp del is likely a hifiasm consensus error since only supported by one read - nearby 51bp ins from same read already excluded													1|2:FN:am:ti:.:SNP:hetalt	1/1:FP:am:ti:1186.77:SNP:homalt	1|2:FN:am:ti:.:SNP:hetalt	1/1:FP:am:ti:1121.77:SNP:homalt	1|2:FN:am:ti:.:SNP:hetalt	1/1:FP:am:ti:30:SNP:homalt	1|2:FN:am:ti:.:SNP:hetalt	1/1:FP:am:ti:1281.03:SNP:homalt	1|2:FN:am:ti:.:SNP:hetalt	1/1:FP:am:ti:0:SNP:homalt	1|2:FN:am:ti:.:SNP:hetalt	1/1:FP:am:ti:164.39:SNP:homalt	1|2:FN:am:ti:.:SNP:hetalt	1/1:FP:am:ti:37:SNP:homalt	10:135235890	133422386
Common		GRCh38			10	chr10	135235890	133422386	1584	FP_FN	T	C,*	GT:BD:BK:BI:QQ:BVT:BLT	1|2:FN:am:ti:.:SNP:hetalt	1/1:FP:am:ti:100:SNP:homalt	CommonFP_FN			no	yes	40bp del is likely a hifiasm consensus error since only supported by one read - nearby 51bp ins from same read already excluded													1|2:FN:am:ti:.:SNP:hetalt	1/1:FP:am:ti:1186.77:SNP:homalt	1|2:FN:am:ti:.:SNP:hetalt	1/1:FP:am:ti:1296.77:SNP:homalt	1|2:FN:am:ti:.:SNP:hetalt	1/1:FP:am:ti:30:SNP:homalt	1|2:FN:am:ti:.:SNP:hetalt	1/1:FP:am:ti:968.03:SNP:homalt	1|2:FN:am:ti:.:SNP:hetalt	1/1:FP:am:ti:0:SNP:homalt	1|2:FN:am:ti:.:SNP:hetalt	1/1:FP:am:ti:164.39:SNP:homalt	1|2:FN:am:ti:.:SNP:hetalt	1/1:FP:am:ti:37:SNP:homalt		135235890
CMH_DRAGEN_3.6.3	NA24385.hard-filtered.vcf.gz	GRCh37	small-variants	INDEL	10	chr10	135237474	133423970	0	FP_FN	A	AGGAGCGCCGCGGTG	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:i6_15:INDEL:homalt	0/1:FP:am:45.15:i6_15:INDEL:het	yes	no		yes	no	14bp ins on almost all reads that cross the region for all techs																											10:135237474	133423970
Segdup. 14bp insertion present in ILMN but coverage drop off significantly nearby, also support for REF. No HP separation for Hifi, 10X and ONT do. All support 14 insertion there just uns	GRCh38_HG002_WGS_union.vcf.gz	GRCh38	small-variants	INDEL	10	chr10	135237474	133423970	0	FP_FN	A	AGGAGCGCCGCGGTG	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:i6_15:INDEL:homalt	0/1:FP:am:0:i6_15:INDEL:het 	unsure	unsure		yes	no	14bp ins on almost all reads that cross the region for all techs				unsure about GT	no	Segdup. 14bp insertion present in ILMN but coverage drop off significantly nearby. no HP separation for Hifi, 10X and ONT do. All support 14 insertion, but only some for REF. Hifi support HOM_VAR. 																						135237474
Common		GRCh38			10	chr10	135237474	133423970	1108	FP_FN	A	AGGAGCGCCGCGGTG	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:100:i6_15:INDEL:homalt	1/1:TP:gm:100:i6_15:INDEL:homalt	CommonFP_FN			yes	no	14bp ins on almost all reads that cross the region for all techs													1|1:TP:gm:1177.73:i6_15:INDEL:homalt	1/1:TP:gm:1177.73:i6_15:INDEL:homalt	1|1:FN:am:.:i6_15:INDEL:homalt	0/1:FP:am:388.73:i6_15:INDEL:het	1|1:TP:gm:30:i6_15:INDEL:homalt	1/1:TP:gm:30:i6_15:INDEL:homalt	1|1:FN:am:.:i6_15:INDEL:homalt	0/1:FP:am:411.64:i6_15:INDEL:het	1|1:FN:am:.:i6_15:INDEL:homalt	0/1:FP:am:0:i6_15:INDEL:het	1|1:FN:am:.:i6_15:INDEL:homalt	0/1:FP:am:45.15:i6_15:INDEL:het	1|1:FN:am:.:i6_15:INDEL:homalt	0/1:FP:am:7:i6_15:INDEL:het		135237474
NCBI	HG002_grch37_dipcall.vcf.gz	GRCh37	small-variants	SNP	10	chr10	135238582	133425078	1237	FP_FN	C	T	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:ti:SNP:homalt	0/1:FP:am:30:ti:SNP:het	unsure	unsure	ILMN reads not supporting SNP here, but 10X for HET; PB for HOM	yes	no	long reads support hom var and only a few 10x reads and likely mismapped short reads support ref so likely mapping error																											10:135238582	133425078
DNAnexus	hs37d5_HG002_WGS_union.vcf.gz	GRCh37	small-variants	INDEL	10	chr10	135239819	133426315	114	FP	ATAAAAC	A	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	1/1:0:FP:.:d6_15:INDEL:homalt	unsure	unsure	Illumina raw data has sufficient reads supporting this deletion. In ONT AND 10X Genomics raw reads, there are still 2 reads each supporting this deletion. However, such deletion is not presented by PacBio data.	yes	no	likely illumina mapping error in seg dup, since little evidence in long reads. Reads supporting it in ONT likely due to random noise																											10:135239819	133426315
Common		GRCh37			10	chr10	135239933	133426429	6542	FP_FN	C	CAAA,CA,CAA	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:100:i1_5:INDEL:homalt	1/1:TP:gm:100:i1_5:INDEL:homalt	CommonFP_FN			yes	no	hifiasm likely correct since supported by HiFi and 10x, and the illumina reads support 1bp ins appear to be mapping errors in seg dup													1|1:TP:gm:1484.73:i1_5:INDEL:homalt	1/1:TP:gm:1484.73:i1_5:INDEL:homalt	1|1:FN:lm:.:i1_5:INDEL:homalt	2/2:FP:lm:467.73:i1_5:INDEL:homalt	1|1:FN:lm:.:i1_5:INDEL:homalt	0/2:FP:lm:30:i1_5:INDEL:het	1|1:FN:lm:.:i1_5:INDEL:homalt	3/2:FP:lm:19.9:i1_5:INDEL:hetalt	1|1:FN:lm:.:i1_5:INDEL:homalt	2/2:FP:lm:0:i1_5:INDEL:homalt	1|1:FN:lm:.:i1_5:INDEL:homalt	2/2:FP:lm:43.77:i1_5:INDEL:homalt	1|1:TP:gm:15:i1_5:INDEL:homalt	1/1:TP:gm:15:i1_5:INDEL:homalt	10:135239933	133426429
Common		GRCh37			10	chr10	135246475	133432971	222	FP	C	T	GT:QQ:BD:BK:BI:BVT:BLT	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	CommonFP			yes	no	likely illumina mapping error in seg dup, since little evidence in long reads. Reads supporting it in ONT likely due to random noise													./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:658.77:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:571.6:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:28.97:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:8:FP:.:ti:SNP:het	10:135246475	133432971
CMH_DRAGEN_3.6.3	NA24385.hard-filtered.vcf.gz	GRCh37	small-variants	INDEL	10	chr10	135246697	133433193	0	FN	A	ACC,ACCC	GT:BD:BK:BI:BVT:BLT:QQ	2|1:FN:.:i1_5:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:0	yes	no		unsure	unsure	illumina is low cov and hifi is noisy in C homopolymer, so not clear, though benchmark may b right																											10:135246697	133433193
Common		GRCh37			10	chr10	135246697	133433193	71125	FN	A	ACC,ACCC	GT:BD:BK:BI:BVT:BLT:QQ	2|1:TP:gm:i1_5:INDEL:hetalt:6.9986	2/1:TP:gm:i1_5:INDEL:hetalt:6.9986	CommonFN			unsure	unsure	illumina is low cov and hifi is noisy in C homopolymer, so not clear, though benchmark may b right													2|1:TP:gm:i1_5:INDEL:hetalt:1823.73	2/1:TP:gm:i1_5:INDEL:hetalt:1823.73	2|1:FN:.:i1_5:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:0	2|1:FN:.:i1_5:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:0	2|1:FN:lm:i1_5:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:0	2|1:FN:lm:i1_5:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:0	2|1:FN:.:i1_5:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:0	2|1:FN:.:i1_5:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:0	10:135246697	133433193
NYGC	HG-002-2x250-b37.recalibrated.haplotypeCalls.vcf.gz	GRCh37	small-variants	INDEL	10	chr10	135317822	133504318	-132850158	FP	GTTGT	G	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:55.73:FP:.:d1_5:INDEL:het 	yes	no																															10:135317822	133504318
BCM-HGSC_xAtlas	HG002.hs37d5.60x.1_merged.vcf.gz	GRCh37	small-variants	INDEL	11	chr11	654160	654160	16771	FN	ACC	A	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:lm:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0 	Yes	No																															11:654160	654160
Common		GRCh37			11	chr11	670931	670931	0	FP_FN	G	GTTTTTT,GTTTTTTTT	GT:BD:BK:BI:QQ:BVT:BLT	1|2:FN:am:i6_15:.:INDEL:hetalt	1/1:FP:am:i6_15:100:INDEL:homalt	CommonFP_FN			unsure	unsure	Illumina supports 6bp and 8bp insertion, but they make the homopolymer longer than 20bp, so we should probably exclude													1|2:FN:.:i6_15:.:INDEL:hetalt	.:.:.:.:0:NOCALL:nocall	1|2:FN:am:i6_15:.:INDEL:hetalt	2/2:FP:am:i6_15:214.73:INDEL:homalt	1|2:FN:am:i6_15:.:INDEL:hetalt	1/1:FP:am:i6_15:30:INDEL:homalt	1|2:FN:am:i6_15:.:INDEL:hetalt	2/2:FP:am:i6_15:54.97:INDEL:homalt	1|2:FN:.:i6_15:.:INDEL:hetalt	.:.:.:.:0:NOCALL:nocall	1|2:TP:gm:i6_15:143.46:INDEL:hetalt	2/1:TP:gm:i6_15:143.46:INDEL:hetalt	1|2:FN:am:i6_15:.:INDEL:hetalt	1/1:FP:am:i6_15:11:INDEL:homalt	11:670931	670931
NCBI	HG002_grch38_dipcall.vcf.gz	GRCh38	small-variants	INDEL	11	chr11	670931	670931	0	FP_FN	G	GTTTTTT,GTTTTTTTT	GT:BD:BK:BI:QQ:BVT:BLT	1|2:FN:am:i6_15:.:INDEL:hetalt	1/1:FP:am:i6_15:30:INDEL:homalt	unsure	unsure	evidence favors HOM; most likely HOM	unsure	unsure	Illumina supports 6bp and 8bp insertion, but they make the homopolymer longer than 20bp, so we should probably exclude				unsure	unsure	HiFi show distribution of insertion size however does appear to be higher/lower number of insertions by haplotype, ONT more variable by HP.  ILMN also has distribution of insertion lengths.  I'm not sure variant or GT are correct in benchmark, I would lean more towards HET however.																						670931
Common		GRCh38			11	chr11	670931	670931	3499	FP_FN	G	GTTTTTT,GTTTTTTTT,GTTTTTTTTT	GT:BD:BK:BI:QQ:BVT:BLT	1|2:FN:am:i6_15:.:INDEL:hetalt	1/1:FP:am:i6_15:100:INDEL:homalt	CommonFP_FN			unsure	unsure	Illumina supports 6bp and 8bp insertion, but they make the homopolymer longer than 20bp, so we should probably exclude													1|2:FN:.:i6_15:.:INDEL:hetalt	.:.:.:.:0:NOCALL:nocall	1|2:FN:am:i6_15:.:INDEL:hetalt	1/1:FP:am:i6_15:139.77:INDEL:homalt	1|2:FN:am:i6_15:.:INDEL:hetalt	1/1:FP:am:i6_15:30:INDEL:homalt	1|2:FN:lm:i6_15:.:INDEL:hetalt	0/3:FP:lm:i6_15:10.5:INDEL:het	1|2:FN:.:i6_15:.:INDEL:hetalt	.:.:.:.:0:NOCALL:nocall	1|2:TP:gm:i6_15:141.67:INDEL:hetalt	2/1:TP:gm:i6_15:141.67:INDEL:hetalt	1|2:FN:am:i6_15:.:INDEL:hetalt	1/1:FP:am:i6_15:11:INDEL:homalt		670931
ITER	ITERteam_small-variation_GRCh38_ILMN-PB-ONT.vcf.gz	GRCh38	small-variants	INDEL	11	chr11	674430	674430	11699	FP	A	AG	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:9.7:FP:lm:i1_5:INDEL:het	Yes	No	Not supported in benchmark by any read, surrounding variants match in both truth and query.							skip																								674430
NYGC	HG-002-2x250-b37.recalibrated.haplotypeCalls.vcf.gz	GRCh37	small-variants	INDEL	11	chr11	686129	686129	0	FP_FN	A	T,*	GT:BD:BK:BI:QQ:BVT:BLT	2|1:FN:am:tv:.:SNP:hetalt	0/1:FP:am:tv:246.77:SNP:het 	yes	yes		yes	no	benchmark supported even by illumina in homopolymer in VNTR																											11:686129	686129
Common		GRCh37			11	chr11	686129	686129	1310080	FP_FN	A	T,*	GT:BD:BK:QQ:BI:BVT:BLT	2|1:FN:am:.:tv:SNP:hetalt	0/1:FP:am:100:tv:SNP:het	CommonFP_FN			yes	no	benchmark supported even by illumina in homopolymer in VNTR													2|1:TP:gm:423.77:tv:SNP:hetalt	0/1:TP:gm:423.77:tv:SNP:het	2|1:FN:am:.:tv:SNP:hetalt	0/1:FP:am:246.77:tv:SNP:het	2|1:FN:am:.:tv:SNP:hetalt	0/1:FP:am:30:tv:SNP:het	2|1:FN:am:.:tv:SNP:hetalt	0/1:FP:am:360.01:tv:SNP:het	2|1:FN:lm:.:tv:SNP:hetalt	.:.:.:0:.:NOCALL:nocall	2|1:FN:am:.:tv:SNP:hetalt	0/1:FP:am:50:tv:SNP:het	2|1:TP:gm:25:tv:SNP:hetalt	0/1:TP:gm:25:tv:SNP:het	11:686129	686129
Common		GRCh38			11	chr11	2017439	1996209	44386581	FN	C	G	GT:BD:BK:QQ:BI:BVT:BLT	1|0:TP:gm:100:tv:SNP:het	0/1:TP:gm:100:tv:SNP:het	CommonFN			yes		In non-coding gene H19 that is duplicated in GRCh38 but not in 37 or other individuals, similar to CBS and KCNE1. 													1|0:FN:.:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall	1|0:FN:.:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall	1|0:TP:gm:30:tv:SNP:het	0/1:TP:gm:30:tv:SNP:het	1|0:TP:gm:38.2:tv:SNP:het	0/1:TP:gm:38.2:tv:SNP:het	1|0:FN:.:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall	1|0:FN:.:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall	1|0:FN:.:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall		2017439
Common		GRCh38			11	chr11	46404340	46382790	16236385	FP	GC	G	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:lm:d1_5:INDEL:het	CommonFP			unsure		All techs are noisy in C homopolymer													./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:119.73:FP:lm:d1_5:INDEL:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	1/1:42.8:FP:lm:d1_5:INDEL:homalt	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:93.45:FP:lm:d1_5:INDEL:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.		46404340
Common		GRCh37			11	chr11	62386647	62619175	0	FP_FN	GA	G	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:100:d1_5:INDEL:het	CommonFP_FN			no	yes	hifiasm misses ref haplotype in homopolymer due to highly homozygous region													1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:390.73:d1_5:INDEL:het	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:377.73:d1_5:INDEL:het	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:30:d1_5:INDEL:het	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:428.6:d1_5:INDEL:het	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:0:d1_5:INDEL:het	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:49.88:d1_5:INDEL:het	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:9:d1_5:INDEL:het	11:62386647	62619175
Common		GRCh38			11	chr11	62386647	62619175	6436353	FP_FN	GA	G	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:100:d1_5:INDEL:het	CommonFP_FN			no	yes	hifiasm misses ref haplotype in homopolymer due to highly homozygous region													1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:390.73:d1_5:INDEL:het	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:377.73:d1_5:INDEL:het	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:30:d1_5:INDEL:het	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:98.6:d1_5:INDEL:het	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:0:d1_5:INDEL:het	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:49.89:d1_5:INDEL:het	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:9:d1_5:INDEL:het		62386647
NYGC	HG-002-2x250-b38.recalibrated.haplotypeCalls.vcf.gz	GRCh38	small-variants	INDEL	11	chr11	68822996	69055528	19595	FN	T	TGTCAGCTCTCCTCCCTCTCCACCATGCAAACTGAGGCCAGTGTGCC	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:.:i16_plus:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0 	yes	no								skip																								68822996
Common		GRCh37			11	chr11	68842591	69075123	0	FP_FN	G	GC	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:100:i1_5:INDEL:het	CommonFP_FN			no	yes	hifiasm misses ref haplotype due to highly homozygous region													1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:490.73:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:837.73:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:30:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:649.64:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:0:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:47.69:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:13:i1_5:INDEL:het	11:68842591	69075123
Common		GRCh38			11	chr11	68842591	69075123	42877	FP_FN	G	GC	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:100:i1_5:INDEL:het	CommonFP_FN			no	yes	hifiasm misses ref haplotype due to highly homozygous region													1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:559.73:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:844.73:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:30:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:501.64:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:0:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:47.69:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:13:i1_5:INDEL:het		68842591
CMH_DRAGEN_3.6.3	NA24385.hard-filtered.vcf.gz	GRCh38	small-variants	INDEL	11	chr11	68885468	69118000	0	FP	C	CATTTATTT,CATTTATTTATTTATTT	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	2/1:281.23:FP:.:i16_plus,i6_15:INDEL:hetalt	unsure	unsure	In repeat. Compared to the truth variant called at chr11:69118038. Only one allele differs. ILMN including 10X supports the query better. PacBio is partly supporting the query but there is one haplotag at the locus.	no	yes	hifiasm error in TR in highly homozygous region, missing 8bp ins on one haplotype and calling 15bp instead of 16bp ins on other haplotype, so that it is at the end of the TR				no	yes	All reads show evidence of some insertion, this looks like compound HET 																						68885468
Common		GRCh38			11	chr11	68885468	69118000	38	FP	C	CATTTATTT,CATTTATTTATTTATTT	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	2/1:100:FP:.:i16_plus,i6_15:INDEL:hetalt	CommonFP			no	yes	hifiasm error in TR in highly homozygous region, missing 8bp ins on one haplotype and calling 15bp instead of 16bp ins on other haplotype, so that it is at the end of the TR													.:.:.:.:.:NOCALL:nocall	2/1:1726.73:FP:.:i16_plus,i6_15:INDEL:hetalt	.:.:.:.:.:NOCALL:nocall	2/1:1219.73:FP:.:i16_plus,i6_15:INDEL:hetalt	.:.:.:.:.:NOCALL:nocall	2/1:30:FP:.:i16_plus,i6_15:INDEL:hetalt	.:.:.:.:.:NOCALL:nocall	2/1:860.1:FP:.:i16_plus,i6_15:INDEL:hetalt	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:.:i6_15:INDEL:het	.:.:.:.:.:NOCALL:nocall	2/1:281.23:FP:.:i16_plus,i6_15:INDEL:hetalt	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.		68885468
Common		GRCh38			11	chr11	68885506	69118038	9222	FN	T	TTTATTTATTTATTTA	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:.:i6_15:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no	yes	hifiasm error in TR in highly homozygous region, missing 8bp ins on one haplotype and calling 15bp instead of 16bp ins on other haplotype, so that it is at the end of the TR													1|1:FN:.:i6_15:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:i6_15:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:i6_15:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:i6_15:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:i6_15:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:i6_15:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:i6_15:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0		68885506
Common		GRCh38			11	chr11	68894728	69127260	-62325958	FN	T	TG	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:lm:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			unsure	unsure	illumina has a lot of reads clipped at homopolymer and HiFi is noisy													0|1:TP:gm:i1_5:INDEL:het:169.73	0/1:TP:gm:i1_5:INDEL:het:169.73	0|1:FN:lm:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0		68894728
Common		GRCh37			12	chr12	6910468	6801302	236	FN	N	A	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:lm:.:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	benchmark is correct, though reference is N													1|1:FN:lm:.:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:lm:.:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:.:SNP:homalt:30	1/1:TP:gm:.:SNP:homalt:30	1|1:FN:lm:.:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:lm:.:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:lm:.:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:lm:.:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	12:6910468	6801302
Common		GRCh37			12	chr12	6910704	6801538	3477	FN	N	G	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:lm:.:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	benchmark is correct, though reference is N													1|1:FN:lm:.:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:lm:.:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:.:SNP:homalt:30	1/1:TP:gm:.:SNP:homalt:30	1|1:FN:lm:.:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:lm:.:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:lm:.:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:lm:.:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	12:6910704	6801538
Common		GRCh37			12	chr12	6914181	6805015	0	FP_FN	CA	C,CAA	GT:BD:BK:BI:QQ:BVT:BLT	1|2:FN:am:d1_5,i1_5:.:INDEL:hetalt	0/1:FP:am:d1_5:100:INDEL:het	CommonFP_FN			no	yes	likely hifiasm error calling 1bp ins instead of ref on one haplotype in long homopolymer													1|2:FN:am:d1_5,i1_5:.:INDEL:hetalt	0/1:FP:am:d1_5:74.77:INDEL:het	1|2:FN:am:d1_5,i1_5:.:INDEL:hetalt	0/1:FP:am:d1_5:121.73:INDEL:het	1|2:FN:am:d1_5,i1_5:.:INDEL:hetalt	1/1:FP:am:d1_5:30:INDEL:homalt	1|2:FN:am:d1_5,i1_5:.:INDEL:hetalt	1/1:FP:am:d1_5:109.44:INDEL:homalt	1|2:FN:am:d1_5,i1_5:.:INDEL:hetalt	0/1:FP:am:d1_5:0:INDEL:het	1|2:FN:am:d1_5,i1_5:.:INDEL:hetalt	0/1:FP:am:d1_5:50:INDEL:het	1|2:FN:am:d1_5,i1_5:.:INDEL:hetalt	0/1:FP:am:d1_5:5:INDEL:het	12:6914181	6805015
Common		GRCh38			12	chr12	6914181	6805015	1782	FP_FN	CA	C,CAA	GT:BD:BK:BI:QQ:BVT:BLT	1|2:FN:am:d1_5,i1_5:.:INDEL:hetalt	0/1:FP:am:d1_5:100:INDEL:het	CommonFP_FN			no	yes	likely hifiasm error calling 1bp ins instead of ref on one haplotype in long homopolymer													1|2:FN:am:d1_5,i1_5:.:INDEL:hetalt	0/1:FP:am:d1_5:74.77:INDEL:het	1|2:FN:am:d1_5,i1_5:.:INDEL:hetalt	0/1:FP:am:d1_5:111.73:INDEL:het	1|2:FN:am:d1_5,i1_5:.:INDEL:hetalt	1/1:FP:am:d1_5:30:INDEL:homalt	1|2:FN:am:d1_5,i1_5:.:INDEL:hetalt	0/1:FP:am:d1_5:131.6:INDEL:het	1|2:FN:am:d1_5,i1_5:.:INDEL:hetalt	0/1:FP:am:d1_5:0:INDEL:het	1|2:FN:am:d1_5,i1_5:.:INDEL:hetalt	0/1:FP:am:d1_5:50:INDEL:het	1|2:FN:am:d1_5,i1_5:.:INDEL:hetalt	0/1:FP:am:d1_5:5:INDEL:het		6914181
NCBI	HG002_grch38_dipcall.vcf.gz	GRCh38	small-variants	SNP	12	chr12	6915963	6806797	396384	FN	T	C	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:lm:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	yes	no	repeat region; het INS 1bp apart for query							skip																								6915963
Roche	RN_HG002_Illumina_PacBio_Oxford_GRCh37.vcf.gz	GRCh37	small-variants	INDEL	12	chr12	7355777	7203181	0	FN	A	AAACTAAACTAAACTAAACTAAACTAAACTACAG	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:lm:i16_plus:INDEL:het:.	.:.:.:.:NOCALL:nocall:0 	yes	no	SV breakpoint	No	yes	While the assembly is correct, a dipcall bug causes this insertion to be called without the adjacent deletion in the benchmark vcf, so should be excluded																											12:7355777	7203181
NYGC	HG-002-2x250-b37.recalibrated.haplotypeCalls.vcf.gz	GRCh37	small-variants	INDEL	12	chr12	7355777	7203181	0	FP	ATGC	A	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:685.73:FP:lm:d1_5:INDEL:het 	unsure		The call isn't correct but there is evidence of a larger deletion here in the pacbio, illumina and 10X datasets. However, there also seems to be some odd alignment in this region.	No	unsure	While the assembly is correct, a dipcall bug causes this insertion to be called without the adjacent deletion in the benchmark vcf, so should be excluded																											12:7355777	7203181
Common		GRCh37			12	chr12	7355777	7203181	0	FP	ATGCACTGCACTG	AACTGCACTG,A	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:lm:d1_5:INDEL:het	CommonFP			No		While the assembly is correct, a dipcall bug causes this insertion to be called without the adjacent deletion in the benchmark vcf, so should be excluded													.:.:.:.:.:NOCALL:nocall	0/1:831.73:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:685.73:FP:lm:d1_5:INDEL:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:604.6:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/2:0:FP:lm:d6_15:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:47.48:FP:lm:d1_5:INDEL:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	12:7355777	7203181
Common		GRCh37			12	chr12	7355777	7203181	0	FN	A	AAACTAAACTAAACTAAACTAAACTAAACTACAG	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:lm:i16_plus:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			No		While the assembly is correct, a dipcall bug causes this insertion to be called without the adjacent deletion in the benchmark vcf, so should be excluded													0|1:FN:lm:i16_plus:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:i16_plus:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:TP:gm:i16_plus:INDEL:het:30	0/1:TP:gm:i16_plus:INDEL:het:30	0|1:FN:lm:i16_plus:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:i16_plus:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:i16_plus:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i16_plus:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	12:7355777	7203181
Common		GRCh38			12	chr12	7355777	7203181	0	FN	A	AAACTAAACTAAACTAAACTAAACTAAACTACAG	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:lm:i16_plus:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			No		While the assembly is correct, a dipcall bug causes this insertion to be called without the adjacent deletion in the benchmark vcf, so should be excluded													.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:i16_plus:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:TP:gm:i16_plus:INDEL:het:30	0/1:TP:gm:i16_plus:INDEL:het:30	0|1:FN:lm:i16_plus:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:i16_plus:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:i16_plus:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i16_plus:INDEL:het:.	.:.:.:.:NOCALL:nocall:0			7355777
Common		GRCh38			12	chr12	7355777	7203181	4	FP	ATGCACTGCACTG	AACTGCACTG,A	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:lm:d1_5:INDEL:het	CommonFP			No		While the assembly is correct, a dipcall bug causes this insertion to be called without the adjacent deletion in the benchmark vcf, so should be excluded													0/1:834.73:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:850.73:FP:lm:d1_5:INDEL:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:1036.6:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/2:0:FP:lm:d6_15:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:47.48:FP:lm:d1_5:INDEL:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.			7355777
Common		GRCh37			12	chr12	7355781	7203185	0	FP	ACTGCACTGC	A	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:lm:d6_15:INDEL:het	CommonFP			No		While the assembly is correct, a dipcall bug causes this insertion to be called without the adjacent deletion in the benchmark vcf, so should be excluded													.:.:.:.:.:NOCALL:nocall	0/1:831.73:FP:lm:d6_15:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:721.73:FP:lm:d6_15:INDEL:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:640.6:FP:lm:d6_15:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:lm:d6_15:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:47.05:FP:lm:d6_15:INDEL:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	12:7355781	7203185
Common		GRCh38			12	chr12	7355781	7203185	13	FP	ACTGCACTGC	A	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:lm:d6_15:INDEL:het	CommonFP			No		While the assembly is correct, a dipcall bug causes this insertion to be called without the adjacent deletion in the benchmark vcf, so should be excluded													0/1:834.73:FP:lm:d6_15:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:885.73:FP:lm:d6_15:INDEL:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:1026.64:FP:lm:d6_15:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:lm:d6_15:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:47.05:FP:lm:d6_15:INDEL:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.			7355781
PacBio_gatk4	gatk4hc_HG002_15kb_20kb_52X_SequelII.vcf.gz	GRCh37	small-variants	SNP	12	chr12	7355794	7203198	0	FP	G	A	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:840.77:FP:lm:ti:SNP:het	unsure	unsure	supported by all reads, not supported by assembly	No		While the assembly is correct, a dipcall bug causes this insertion to be called without the adjacent deletion in the benchmark vcf, so should be excluded																											12:7355794	7203198
Common		GRCh37			12	chr12	7355794	7203198	0	FP	G	A	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:8.1761:FP:lm:ti:SNP:het	CommonFP			No		While the assembly is correct, a dipcall bug causes this insertion to be called without the adjacent deletion in the benchmark vcf, so should be excluded													.:.:.:.:.:NOCALL:nocall	0/1:840.77:FP:lm:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:733.77:FP:lm:ti:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:685.6:FP:lm:ti:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:44.88:FP:lm:ti:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	12:7355794	7203198
Common		GRCh38			12	chr12	7355794	7203198	1	FP	G	A	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:9.8606:FP:lm:ti:SNP:het	CommonFP			No		While the assembly is correct, a dipcall bug causes this insertion to be called without the adjacent deletion in the benchmark vcf, so should be excluded													0/1:843.77:FP:lm:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:897.77:FP:lm:ti:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:774.6:FP:lm:ti:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:44.88:FP:lm:ti:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.			7355794
Common		GRCh37			12	chr12	7355795	7203199	0	FP	C	A	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:8.1761:FP:lm:tv:SNP:het	CommonFP			No		While the assembly is correct, a dipcall bug causes this insertion to be called without the adjacent deletion in the benchmark vcf, so should be excluded													.:.:.:.:.:NOCALL:nocall	0/1:840.77:FP:lm:tv:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:730.77:FP:lm:tv:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:685.6:FP:lm:tv:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:44.88:FP:lm:tv:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	12:7355795	7203199
Common		GRCh38			12	chr12	7355795	7203199	4	FP	C	A	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:9.8606:FP:lm:tv:SNP:het	CommonFP			No		While the assembly is correct, a dipcall bug causes this insertion to be called without the adjacent deletion in the benchmark vcf, so should be excluded													0/1:843.77:FP:lm:tv:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:894.77:FP:lm:tv:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:771.6:FP:lm:tv:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:44.88:FP:lm:tv:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.			7355795
Common		GRCh37			12	chr12	7355799	7203203	0	FP	G	A	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:8.1761:FP:lm:ti:SNP:het	CommonFP			No		While the assembly is correct, a dipcall bug causes this insertion to be called without the adjacent deletion in the benchmark vcf, so should be excluded													.:.:.:.:.:NOCALL:nocall	0/1:840.77:FP:lm:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:733.77:FP:lm:ti:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:688.6:FP:lm:ti:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:44.88:FP:lm:ti:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	12:7355799	7203203
CMH_DRAGEN_3.6.3	NA24385.hard-filtered.vcf.gz	GRCh38	small-variants	SNP	12	chr12	7355799	7203203	0	FP	G	A	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:44.88:FP:lm:ti:SNP:het	yes	unsure	Possibly an alternative representation, though not parsimonious	No	yes	While the assembly is correct, a dipcall bug causes this insertion to be called without the adjacent deletion in the benchmark vcf, so should be excluded																												7355799
NYGC	HG-002-2x250-b38.recalibrated.haplotypeCalls.vcf.gz	GRCh38	small-variants	SNP	12	chr12	7355799	7203203	0	FP	G	A	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:897.77:FP:lm:ti:SNP:het 	yes	no		No	yes	While the assembly is correct, a dipcall bug causes this insertion to be called without the adjacent deletion in the benchmark vcf, so should be excluded				skip																								7355799
Common		GRCh38			12	chr12	7355799	7203203	5	FP	G	A	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:9.8606:FP:lm:ti:SNP:het	CommonFP			No		While the assembly is correct, a dipcall bug causes this insertion to be called without the adjacent deletion in the benchmark vcf, so should be excluded													0/1:843.77:FP:lm:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:897.77:FP:lm:ti:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:1111.6:FP:lm:ti:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:44.88:FP:lm:ti:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.			7355799
NYGC	HG-002-2x250-b37.recalibrated.haplotypeCalls.vcf.gz	GRCh37	small-variants	SNP	12	chr12	7355804	7203208	0	FP	G	A	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:652.77:FP:lm:ti:SNP:het 	yes	no		No	yes	While the assembly is correct, a dipcall bug causes this insertion to be called without the adjacent deletion in the benchmark vcf, so should be excluded																											12:7355804	7203208
NYGC	HG-002-2x250-b38.recalibrated.haplotypeCalls.vcf.gz	GRCh38	small-variants	SNP	12	chr12	7355804	7203208	1	FP	G	A	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:817.77:FP:lm:ti:SNP:het 	yes	no		No	yes	While the assembly is correct, a dipcall bug causes this insertion to be called without the adjacent deletion in the benchmark vcf, so should be excluded				skip																								7355804
CMH_DRAGEN_3.6.3	NA24385.hard-filtered.vcf.gz	GRCh37	small-variants	SNP	12	chr12	7355805	7203209	0	FP	C	A	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:47.48:FP:lm:tv:SNP:het	unsure	unsure	In tr. Possibly alternative representation of the benchmark's indel at 7355777 as some eveidences are shown in PacBio/Nanopore.																														12:7355805	7203209
NYGC	HG-002-2x250-b38.recalibrated.haplotypeCalls.vcf.gz	GRCh38	small-variants	SNP	12	chr12	7355805	7203209	4	FP	C	A	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:817.77:FP:lm:tv:SNP:het 	yes	no		No	yes	While the assembly is correct, a dipcall bug causes this insertion to be called without the adjacent deletion in the benchmark vcf, so should be excluded				skip																								7355805
Common		GRCh38			12	chr12	7355809	7203213	1	FP	G	A	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:11.9504:FP:.:ti:SNP:het	CommonFP			No		While the assembly is correct, a dipcall bug causes this insertion to be called without the adjacent deletion in the benchmark vcf, so should be excluded													0/1:843.77:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:775.77:FP:.:ti:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:1063.6:FP:.:ti:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:47.49:FP:.:ti:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.			7355809
Roche	RN_HG002_Illumina_PacBio_Oxford_GRCh37.vcf.gz	GRCh37	small-variants	SNP	12	chr12	7355810	7203214	0	FP	C	A	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:17.0292:FP:.:tv:SNP:het 	yes	no		No	yes	While the assembly is correct, a dipcall bug causes this insertion to be called without the adjacent deletion in the benchmark vcf, so should be excluded																											12:7355810	7203214
Common		GRCh37			12	chr12	7355810	7203214	0	FP	C	A	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:17.0292:FP:.:tv:SNP:het	CommonFP			No	yes	While the assembly is correct, a dipcall bug causes this insertion to be called without the adjacent deletion in the benchmark vcf, so should be excluded													.:.:.:.:.:NOCALL:nocall	0/1:840.77:FP:.:tv:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:610.77:FP:.:tv:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:688.6:FP:.:tv:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:48.48:FP:.:tv:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	12:7355810	7203214
CMH_DRAGEN_3.6.3	NA24385.hard-filtered.vcf.gz	GRCh38	small-variants	SNP	12	chr12	7355810	7203214	0	FP	C	A	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:48.48:FP:.:tv:SNP:het	yes	unsure	Possibly an alternative representation, though not parsimonious	No	yes	While the assembly is correct, a dipcall bug causes this insertion to be called without the adjacent deletion in the benchmark vcf, so should be excluded																												7355810
Common		GRCh38			12	chr12	7355810	7203214	4	FP	C	A	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:18.11:FP:.:tv:SNP:het	CommonFP			No		While the assembly is correct, a dipcall bug causes this insertion to be called without the adjacent deletion in the benchmark vcf, so should be excluded													0/1:843.77:FP:.:tv:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:775.77:FP:.:tv:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:1063.6:FP:.:tv:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:48.48:FP:.:tv:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.			7355810
Common		GRCh37			12	chr12	7355814	7203218	0	FP	G	A	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:17.0292:FP:.:ti:SNP:het	CommonFP			No		While the assembly is correct, a dipcall bug causes this insertion to be called without the adjacent deletion in the benchmark vcf, so should be excluded													.:.:.:.:.:NOCALL:nocall	0/1:840.77:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:610.77:FP:.:ti:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:691.6:FP:.:ti:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:49.46:FP:.:ti:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	12:7355814	7203218
Common		GRCh38			12	chr12	7355814	7203218	1	FP	G	A	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:18.11:FP:.:ti:SNP:het	CommonFP			No		While the assembly is correct, a dipcall bug causes this insertion to be called without the adjacent deletion in the benchmark vcf, so should be excluded													0/1:843.77:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:775.77:FP:.:ti:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:1063.6:FP:.:ti:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:49.46:FP:.:ti:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.			7355814
Common		GRCh37			12	chr12	7355815	7203219	0	FP	C	A	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:17.0292:FP:.:tv:SNP:het	CommonFP			No		While the assembly is correct, a dipcall bug causes this insertion to be called without the adjacent deletion in the benchmark vcf, so should be excluded													.:.:.:.:.:NOCALL:nocall	0/1:840.77:FP:.:tv:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:610.77:FP:.:tv:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:688.6:FP:.:tv:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:49.45:FP:.:tv:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	12:7355815	7203219
Common		GRCh38			12	chr12	7355815	7203219	5	FP	C	A	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:18.11:FP:.:tv:SNP:het	CommonFP			No		While the assembly is correct, a dipcall bug causes this insertion to be called without the adjacent deletion in the benchmark vcf, so should be excluded													0/1:843.77:FP:.:tv:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:775.77:FP:.:tv:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:1063.6:FP:.:tv:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:49.45:FP:.:tv:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.			7355815
Common		GRCh37			12	chr12	7355820	7203224	0	FP	CATT	C	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:35.2289:FP:.:d1_5:INDEL:het	CommonFP			No		While the assembly is correct, a dipcall bug causes this insertion to be called without the adjacent deletion in the benchmark vcf, so should be excluded													.:.:.:.:.:NOCALL:nocall	0/1:831.73:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:559.73:FP:.:d1_5:INDEL:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:669.6:FP:.:d1_5:INDEL:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:47.81:FP:.:d1_5:INDEL:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	12:7355820	7203224
CMH_DRAGEN_3.6.3	NA24385.hard-filtered.vcf.gz	GRCh38	small-variants	INDEL	12	chr12	7355820	7203224	0	FP	CATT	C	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:47.81:FP:.:d1_5:INDEL:het	yes	unsure	Possibly an alternative representation of the truth variant at chr12:7203181.	No	yes	While the assembly is correct, a dipcall bug causes this insertion to be called without the adjacent deletion in the benchmark vcf, so should be excluded																												7355820
Common		GRCh38			12	chr12	7355820	7203224	5	FP	CATT	C	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:33.0101:FP:.:d1_5:INDEL:het	CommonFP			No		While the assembly is correct, a dipcall bug causes this insertion to be called without the adjacent deletion in the benchmark vcf, so should be excluded													0/1:834.73:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:724.73:FP:.:d1_5:INDEL:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:1060.6:FP:.:d1_5:INDEL:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:47.81:FP:.:d1_5:INDEL:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.			7355820
Common		GRCh37			12	chr12	7355825	7203229	0	FP	C	G	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:10.8955:FP:.:tv:SNP:het	CommonFP			No		While the assembly is correct, a dipcall bug causes this insertion to be called without the adjacent deletion in the benchmark vcf, so should be excluded													.:.:.:.:.:NOCALL:nocall	0/1:841.77:FP:.:tv:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:568.77:FP:.:tv:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:672.6:FP:.:tv:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:44.99:FP:.:tv:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	12:7355825	7203229
Roche	RN_HG002_Illumina_PacBio_Oxford.vcf.gz	GRCh38	small-variants	SNP	12	chr12	7355825	7203229	0	FP	C	G	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:10.7192:FP:.:tv:SNP:het 	yes	no	SV breakpoint	No	yes	While the assembly is correct, a dipcall bug causes this insertion to be called without the adjacent deletion in the benchmark vcf, so should be excluded				skip																								7355825
Common		GRCh38			12	chr12	7355825	7203229	6379	FP	C	G	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:10.7192:FP:.:tv:SNP:het	CommonFP			No		While the assembly is correct, a dipcall bug causes this insertion to be called without the adjacent deletion in the benchmark vcf, so should be excluded													0/1:844.77:FP:.:tv:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:733.77:FP:.:tv:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:1060.6:FP:.:tv:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:44.99:FP:.:tv:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.			7355825
BCM-HGSC_xAtlas	HG002.GRCh38.60x.1_merged.vcf.gz	GRCh38	small-variants	INDEL	12	chr12	7362204	7209608	451429	FP_FN	G	T,GCTGAGTCGGTGGAGTAATGTGCAGAGTTTGAT	GT:BD:BK:QQ:BI:BVT:BLT	2|2:FN:am:.:i16_plus:INDEL:homalt	0/1:FP:lm:19:tv:SNP:het 	Yes	No								skip																								7362204
Common		GRCh37			12	chr12	7813633	7661037	0	FP_FN	C	CA,CAA	GT:BD:BK:QQ:BI:BVT:BLT	2|2:FN:am:.:i1_5:INDEL:homalt	2/1:FP:am:100:i1_5:INDEL:hetalt	CommonFP_FN			no	yes	hifiasm error on one haplotype likely due to noisy homopolymer since not highly homozygous													2|2:TP:gm:253.73:i1_5:INDEL:homalt	2/2:TP:gm:253.73:i1_5:INDEL:homalt	2|2:FN:am:.:i1_5:INDEL:homalt	2/1:FP:am:666.73:i1_5:INDEL:hetalt	2|2:TP:gm:30:i1_5:INDEL:homalt	2/2:TP:gm:30:i1_5:INDEL:homalt	2|2:TP:gm:110.1:i1_5:INDEL:homalt	2/2:TP:gm:110.1:i1_5:INDEL:homalt	2|2:FN:am:.:i1_5:INDEL:homalt	0/2:FP:am:0:i1_5:INDEL:het	2|2:FN:am:.:i1_5:INDEL:homalt	2/1:FP:am:107.49:i1_5:INDEL:hetalt	2|2:FN:lm:.:i1_5:INDEL:homalt	1/1:FP:lm:10:i1_5:INDEL:homalt	12:7813633	7661037
Common		GRCh38			12	chr12	7813633	7661037	3863	FP_FN	C	CA,CAA	GT:BD:BK:QQ:BI:BVT:BLT	2|2:FN:am:.:i1_5:INDEL:homalt	2/1:FP:am:100:i1_5:INDEL:hetalt	CommonFP_FN			no	yes	hifiasm error on one haplotype likely due to noisy homopolymer since not highly homozygous													2|2:TP:gm:253.73:i1_5:INDEL:homalt	2/2:TP:gm:253.73:i1_5:INDEL:homalt	2|2:FN:am:.:i1_5:INDEL:homalt	2/1:FP:am:728.73:i1_5:INDEL:hetalt	2|2:TP:gm:30:i1_5:INDEL:homalt	2/2:TP:gm:30:i1_5:INDEL:homalt	2|2:FN:.:.:i1_5:INDEL:homalt	.:.:.:0:.:NOCALL:nocall	2|2:FN:am:.:i1_5:INDEL:homalt	0/2:FP:am:0:i1_5:INDEL:het	2|2:FN:am:.:i1_5:INDEL:homalt	2/1:FP:am:106.72:i1_5:INDEL:hetalt	2|2:FN:lm:.:i1_5:INDEL:homalt	1/1:FP:lm:10:i1_5:INDEL:homalt		7813633
Roche	RN_HG002_Illumina_PacBio_Oxford_GRCh37.vcf.gz	GRCh37	small-variants	INDEL	12	chr12	7817496	7664900	0	FP_FN	T	TA	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:100:i1_5:INDEL:het 	no	yes	from ILM, 10X and PB haplotyepe tags it seems HET to me.	no	yes	hifiasm error on one haplotype likely due to noisy homopolymer since not highly homozygous																											12:7817496	7664900
Common		GRCh37			12	chr12	7817496	7664900	0	FP_FN	T	TA	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:100:i1_5:INDEL:het	CommonFP_FN			no	yes	hifiasm error on one haplotype likely due to noisy homopolymer since not highly homozygous													1|1:FN:.:.:i1_5:INDEL:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:141.73:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:30:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:131.64:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:0:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:50:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:7:i1_5:INDEL:het	12:7817496	7664900
Common		GRCh38			12	chr12	7817496	7664900	26894	FP_FN	T	TA	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:100:i1_5:INDEL:het	CommonFP_FN			no	yes	hifiasm error on one haplotype likely due to noisy homopolymer since not highly homozygous													1|1:FN:.:.:i1_5:INDEL:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:158.73:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:30:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:193.64:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:0:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:50:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:7:i1_5:INDEL:het		7817496
DNAnexus	GRCh38_HG002_WGS_union.vcf.gz	GRCh38	small-variants	INDEL	12	chr12	7844390	7691794	42421113	FN	TGAG	T	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:lm:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0 	yes	no	The variant is called by all short-read variant callers. It didn't get included in the VCF because the variant representation formatting issue.							skip																								7844390
DNAnexus	GRCh38_HG002_WGS_union.vcf.gz	GRCh38	small-variants	INDEL	12	chr12	50506690	50112907	396	FP	C	CGTTATGTTATGTTAT	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	1/1:0:FP:lm:i6_15:INDEL:homalt 	yes	yes	Both benchmark set and query callset are right. The differences is due to VCF variant record formatting.	yes	no	benchmark correctly calls 15bp ins and 5bp del in TR; query miscalls part																												50506690
Common		GRCh37			12	chr12	50507086	50113303	0	FP	AT	A	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:.:d1_5:INDEL:het	CommonFP			no	yes	benchmark misses del in long homopolymer due to noise in HiFi													./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:344.73:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:308.6:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:43.38:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:12:FP:.:d1_5:INDEL:het	12:50507086	50113303
Common		GRCh38			12	chr12	50507086	50113303	916	FP	AT	A	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:.:d1_5:INDEL:het	CommonFP			no	yes	benchmark misses del in long homopolymer due to noise in HiFi													./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:327.73:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:263.6:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:43.39:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:12:FP:.:d1_5:INDEL:het		50507086
BCM-HGSC_xAtlas	HG002.hs37d5.60x.1_merged.vcf.gz	GRCh37	small-variants	INDEL	12	chr12	50508002	50114219	0	FP_FN	G	GA,GAA	GT:BD:BK:QQ:BI:BVT:BLT	2|0:FN:lm:.:i1_5:INDEL:het	0/1:FP:lm:9:i1_5:INDEL:het 	Yes	No		no	yes	benchmark has 2bp instead of 1bp het ins due to noisy homopolymer in HiFi, but illumina is clear																											12:50508002	50114219
Common		GRCh37			12	chr12	50508002	50114219	0	FP_FN	G	GA,GAA	GT:BD:BK:QQ:BI:BVT:BLT	2|0:FN:lm:.:i1_5:INDEL:het	0/1:FP:lm:100:i1_5:INDEL:het	CommonFP_FN			no	yes	benchmark has 2bp instead of 1bp het ins due to noisy homopolymer in HiFi, but illumina is clear													2|0:FN:.:.:i1_5:INDEL:het	.:.:.:0:.:NOCALL:nocall	2|0:FN:lm:.:i1_5:INDEL:het	0/1:FP:lm:85.73:i1_5:INDEL:het	2|0:FN:lm:.:i1_5:INDEL:het	0/1:FP:lm:30:i1_5:INDEL:het	2|0:FN:lm:.:i1_5:INDEL:het	0/1:FP:lm:133.64:i1_5:INDEL:het	2|0:FN:lm:.:i1_5:INDEL:het	0/1:FP:lm:0:i1_5:INDEL:het	2|0:FN:lm:.:i1_5:INDEL:het	0/1:FP:lm:50:i1_5:INDEL:het	2|0:FN:lm:.:i1_5:INDEL:het	0/1:FP:lm:9:i1_5:INDEL:het	12:50508002	50114219
CMH_DRAGEN_3.6.3	NA24385.hard-filtered.vcf.gz	GRCh38	small-variants	INDEL	12	chr12	50508002	50114219	0	FP_FN	G	GA,GAA	GT:BD:BK:QQ:BI:BVT:BLT	2|0:FN:lm:.:i1_5:INDEL:het	0/1:FP:lm:50:i1_5:INDEL:het	unsure	unsure	PacBio supports the truth better but not confident. Confliting evidences exist in most datasets. At the edge of a repeat.	no	yes	benchmark has 2bp instead of 1bp het ins due to noisy homopolymer in HiFi, but illumina is clear				no	yes	appears to be HET but ILMN supports 1bp insertsion not 2.  ILMN reads also cover homopolymer.  Third gen reads support benchmark ALT (2bp) but also support additional insertions.																						50508002
Common		GRCh38			12	chr12	50508002	50114219	6611718	FP_FN	G	GA,GAA	GT:BD:BK:QQ:BI:BVT:BLT	2|0:FN:lm:.:i1_5:INDEL:het	0/1:FP:lm:100:i1_5:INDEL:het	CommonFP_FN			no	yes	benchmark has 2bp instead of 1bp het ins due to noisy homopolymer in HiFi, but illumina is clear													2|0:FN:.:.:i1_5:INDEL:het	.:.:.:0:.:NOCALL:nocall	2|0:FN:lm:.:i1_5:INDEL:het	0/1:FP:lm:88.73:i1_5:INDEL:het	2|0:FN:lm:.:i1_5:INDEL:het	0/1:FP:lm:30:i1_5:INDEL:het	2|0:FN:.:.:i1_5:INDEL:het	.:.:.:0:.:NOCALL:nocall	2|0:FN:lm:.:i1_5:INDEL:het	0/1:FP:lm:0:i1_5:INDEL:het	2|0:FN:lm:.:i1_5:INDEL:het	0/1:FP:lm:50:i1_5:INDEL:het	2|0:FN:lm:.:i1_5:INDEL:het	0/1:FP:lm:9:i1_5:INDEL:het		50508002
Common		GRCh37			12	chr12	57119721	56725937	6874674	FN	G	GC	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:am:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			unsure	unsure	all techs noisy in adjacent G and A homopolymers													1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:lm:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:lm:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	1|0:FN:lm:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	12:57119721	56725937
PacBio_gatk4	gatk4hc_HG002_15kb_20kb_53X_SequelII.vcf.gz	GRCh38	small-variants	INDEL	12	chr12	63994391	63600611	57875505	FP_FN	CTT	C,CTTT	GT:BD:BK:BI:QQ:BVT:BLT	2|1:FN:am:d1_5,i1_5:.:INDEL:hetalt	0/1:FP:am:d1_5:159.73:INDEL:het	yes	no	GATK call should be ./1, since multiallelics are decomposed.							skip																								63994391
PacBio_gatk4	gatk4hc_HG002_15kb_20kb_52X_SequelII.vcf.gz	GRCh37	small-variants	INDEL	12	chr12	121913919	121476116	15677	FP	GAAAC	G	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:730.73:FP:lm:d1_5:INDEL:het	yes	no																															12:121913919	121476116
Common		GRCh37			12	chr12	121929596	121491793	0	FN	C	CA	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no	yes	hifiasm error on one haplotype likely due to noisy homopolymer since heterozygous													0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	12:121929596	121491793
Common		GRCh38			12	chr12	121929596	121491793	13492	FN	C	CA	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no	yes	hifiasm error on one haplotype likely due to noisy homopolymer since heterozygous													0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0		121929596
Common		GRCh37			12	chr12	121943088	121505285	0	FP_FN	C	CA	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:100:i1_5:INDEL:het	CommonFP_FN			no	yes	hifiasm error on one haplotype likely due to noisy homopolymer since not highly homozygous													1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:56.73:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:229.73:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:30:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:138.64:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:0:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:46.75:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:9:i1_5:INDEL:het	12:121943088	121505285
Common		GRCh38			12	chr12	121943088	121505285	67841	FP_FN	C	CA	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:100:i1_5:INDEL:het	CommonFP_FN			no	yes	hifiasm error on one haplotype likely due to noisy homopolymer since not highly homozygous													1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:61.73:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:302.77:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:30:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:132.64:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:0:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:46.75:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:9:i1_5:INDEL:het		121943088
Common		GRCh37			12	chr12	122011031	121573126	0	FP	A	AT	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:.:i1_5:INDEL:het	CommonFP			no	yes	cluster of 3 hifiasm errors on one haplotype likely due to noisy homopolymers and/or consensus errors since not highly homozygous													.:.:.:.:.:NOCALL:nocall	0/1:132.73:FP:.:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:240.73:FP:.:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:.:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:183.64:FP:.:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:.:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:50:FP:.:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:10:FP:.:i1_5:INDEL:het	12:122011031	121573126
Common		GRCh38			12	chr12	122011031	121573126	159	FP	A	AT	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:.:i1_5:INDEL:het	CommonFP			no	yes	cluster of 3 hifiasm errors on one haplotype likely due to noisy homopolymers and/or consensus errors since not highly homozygous													.:.:.:.:.:NOCALL:nocall	0/1:132.73:FP:.:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:250.73:FP:.:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:.:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:206.64:FP:.:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:.:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:50:FP:.:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:10:FP:.:i1_5:INDEL:het		122011031
Common		GRCh37			12	chr12	122011190	121573285	0	FP	CT	C	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:.:d1_5:INDEL:het	CommonFP			no	yes	cluster of 3 hifiasm errors on one haplotype likely due to noisy homopolymers and/or consensus errors since not highly homozygous													.:.:.:.:.:NOCALL:nocall	0/1:119.73:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:237.73:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:271.6:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:49.91:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:12:FP:.:d1_5:INDEL:het	12:122011190	121573285
Common		GRCh38			12	chr12	122011190	121573285	302	FP	CT	C	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:.:d1_5:INDEL:het	CommonFP			no	yes	cluster of 3 hifiasm errors on one haplotype likely due to noisy homopolymers and/or consensus errors since not highly homozygous													.:.:.:.:.:NOCALL:nocall	0/1:119.73:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:237.73:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:249.6:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:49.9:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:12:FP:.:d1_5:INDEL:het		122011190
Common		GRCh37			12	chr12	122011492	121573587	0	FP	CT	C	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:.:d1_5:INDEL:het	CommonFP			no	yes	cluster of 3 hifiasm errors on one haplotype likely due to noisy homopolymers and/or consensus errors since not highly homozygous													.:.:.:.:.:NOCALL:nocall	0/1:263.73:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:447.73:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:208.6:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:50:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:9:FP:.:d1_5:INDEL:het	12:122011492	121573587
Common		GRCh38			12	chr12	122011492	121573587	11206256	FP	CT	C	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:.:d1_5:INDEL:het	CommonFP			no	yes	cluster of 3 hifiasm errors on one haplotype likely due to noisy homopolymers and/or consensus errors since not highly homozygous													.:.:.:.:.:NOCALL:nocall	0/1:263.73:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:438.73:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:124.6:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:50:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:10:FP:.:d1_5:INDEL:het		122011492
DNAnexus	hs37d5_HG002_WGS_union.vcf.gz	GRCh37	small-variants	INDEL	12	chr12	133356429	132779843	12	FN	A	ACC	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:lm:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	yes	no																															12:133356429	132779843
ITER	ITERteam_small-variation_GRCh37_ILMN-PB-ONT.vcf.gz	GRCh37	small-variants	SNP	12	chr12	133356441	132779855	3390	FP	A	G	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:198.02:FP:lm:ti:SNP:het	Yes	No																															12:133356441	132779855
DNAnexus	GRCh38_HG002_WGS_union.vcf.gz	GRCh38	small-variants	INDEL	12	chr12	133359831	132783245	-19668914	FP	A	ACAACCCTGCGAT	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:lm:i6_15:INDEL:het 	yes	no								skip																								133359831
Roche	RN_HG002_Illumina_PacBio_Oxford_GRCh37.vcf.gz	GRCh37	small-variants	INDEL	13	chr13	113768645	113114331	-71712325	FP_FN	TG	T	GT:BD:BK:QQ:BI:BVT:BLT	1|0:FN:am:.:d1_5:INDEL:het	1/1:FP:am:39.9993:d1_5:INDEL:homalt 	unsure	no	From ILM and 10x, it seems that the correct variant in this regioin is multiallelic deletions as: 13-113768642-GTTTG-TTT,GTTT	no	no	illumina indicates benchmark should have 2bp del instead of 1bp del on one haplotype																											13:113768645	113114331
Common		GRCh37			15	chr15	41694204	41402006	0	FP_FN	AT	A	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:100:d1_5:INDEL:het	CommonFP_FN			no	yes	hifiasm misses ref haplotype in homopolymer due to highly homozygous region													1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:585.73:d1_5:INDEL:het	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:508.73:d1_5:INDEL:het	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:30:d1_5:INDEL:het	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:610.6:d1_5:INDEL:het	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:0:d1_5:INDEL:het	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:50:d1_5:INDEL:het	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:13:d1_5:INDEL:het	15:41694204	41402006
Common		GRCh38			15	chr15	41694204	41402006	2140295	FP_FN	AT	A	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:100:d1_5:INDEL:het	CommonFP_FN			no	yes	hifiasm misses ref haplotype in homopolymer due to highly homozygous region													1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:585.73:d1_5:INDEL:het	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:508.73:d1_5:INDEL:het	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:30:d1_5:INDEL:het	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:213.6:d1_5:INDEL:het	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:0:d1_5:INDEL:het	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:50:d1_5:INDEL:het	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:13:d1_5:INDEL:het		41694204
Common		GRCh37			15	chr15	43834499	43542301	0	FP	CGG	C	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:lm:d1_5:INDEL:het	CommonFP			no	yes	hifiasm misses 2bp del in homopolymer on opposite haplotype due to highly homozygous region													./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:1032.73:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:614.06:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:206.83:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:15:FP:lm:d1_5:INDEL:het	15:43834499	43542301
Common		GRCh37			15	chr15	43834499	43542301	0	FN	CG	C	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:am:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no	yes	hifiasm misses 2bp del in homopolymer on opposite haplotype due to highly homozygous region													1|1:FN:.:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:am:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:am:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:am:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:am:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:am:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:lm:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	15:43834499	43542301
Common		GRCh38			15	chr15	43834499	43542301	0	FN	CG	C	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:am:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no	yes	hifiasm misses 2bp del in homopolymer on opposite haplotype due to highly homozygous region													1|1:FN:.:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:am:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:am:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:am:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:am:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:am:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:lm:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0		43834499
Common		GRCh38			15	chr15	43834499	43542301	1	FP	CGG	C	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:lm:d1_5:INDEL:het	CommonFP			no	yes	hifiasm misses 2bp del in homopolymer on opposite haplotype due to highly homozygous region													./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:1007.73:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:594.06:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:204.54:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:16:FP:lm:d1_5:INDEL:het		43834499
Common		GRCh37			15	chr15	43834500	43542302	0	FP	GG	G	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:am:d1_5:INDEL:het	CommonFP			no	yes	hifiasm misses 2bp del in homopolymer on opposite haplotype due to highly homozygous region													./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:1032.73:FP:am:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:am:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:614.06:FP:am:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:am:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:206.83:FP:am:d1_5:INDEL:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	15:43834500	43542302
NYGC	HG-002-2x250-b38.recalibrated.haplotypeCalls.vcf.gz	GRCh38	small-variants	INDEL	15	chr15	43834500	43542302	0	FP	GG	G	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:1007.73:FP:am:d1_5:INDEL:het 	unsure		This is in a LINE. There are 3 alleles present in the 10X and PacBio and only the 2 deletion types in the 2x250bp data.	no	yes	hifiasm misses 2bp del in homopolymer on opposite haplotype due to highly homozygous region				no	yes	LINE and homopolymer G, all support some deletion (1 or 2) and Ref.  This mixture is seen between haplotypes. Unsure of variant but appears to be HET. However coverage does drop significantly for all technologies at this position. 																						43834500
Common		GRCh38			15	chr15	43834500	43542302	345	FP	GG	G	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:am:d1_5:INDEL:het	CommonFP			no	yes	hifiasm misses 2bp del in homopolymer on opposite haplotype due to highly homozygous region													./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:1007.73:FP:am:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:am:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:594.06:FP:am:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:am:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:204.54:FP:am:d1_5:INDEL:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.		43834500
Common		GRCh37			15	chr15	43834845	43542647	0	FP_FN	A	AGTGT,AGT	GT:BD:BK:QQ:BI:BVT:BLT	2|2:FN:am:.:i1_5:INDEL:homalt	1/2:FP:am:100:i1_5:INDEL:hetalt	CommonFP_FN			no	yes	hifiasm misses 4bp ins in TR on opposite haplotype due to highly homozygous region and noisy diTR													2|2:TP:gm:467.73:i1_5:INDEL:homalt	2/2:TP:gm:467.73:i1_5:INDEL:homalt	2|2:FN:am:.:i1_5:INDEL:homalt	1/2:FP:am:678.73:i1_5:INDEL:hetalt	2|2:FN:am:.:i1_5:INDEL:homalt	1/2:FP:am:30:i1_5:INDEL:hetalt	2|2:FN:am:.:i1_5:INDEL:homalt	1/2:FP:am:304.1:i1_5:INDEL:hetalt	.:.:.:.:.:NOCALL:nocall	1/2:FP:lm:0:i1_5:INDEL:hetalt	2|2:FN:am:.:i1_5:INDEL:homalt	1/2:FP:am:133.11:i1_5:INDEL:hetalt	2|2:FN:lm:.:i1_5:INDEL:homalt	0/1:FP:lm:6:i1_5:INDEL:het	15:43834845	43542647
Common		GRCh38			15	chr15	43834845	43542647	11985	FP_FN	A	AGT,AGTGT	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:i1_5:INDEL:homalt	2/1:FP:am:100:i1_5:INDEL:hetalt	CommonFP_FN			no	yes	hifiasm misses 4bp ins in TR on opposite haplotype due to highly homozygous region and noisy diTR													1|1:TP:gm:467.73:i1_5:INDEL:homalt	1/1:TP:gm:467.73:i1_5:INDEL:homalt	1|1:FN:am:.:i1_5:INDEL:homalt	2/1:FP:am:637.73:i1_5:INDEL:hetalt	1|1:FN:am:.:i1_5:INDEL:homalt	2/1:FP:am:30:i1_5:INDEL:hetalt	1|1:FN:am:.:i1_5:INDEL:homalt	2/1:FP:am:499.1:i1_5:INDEL:hetalt	.:.:.:.:.:NOCALL:nocall	2/1:FP:lm:0:i1_5:INDEL:hetalt	1|1:FN:am:.:i1_5:INDEL:homalt	2/1:FP:am:132.77:i1_5:INDEL:hetalt	1|1:FN:lm:.:i1_5:INDEL:homalt	0/2:FP:lm:6:i1_5:INDEL:het		43834845
Common		GRCh37			15	chr15	43846830	43554632	0	FP	CAG	C	GT:QQ:BD:BK:BI:BVT:BLT	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	CommonFP			no	yes	hifiasm misses del in homopolymer on opposite haplotype due to highly homozygous region													.:.:.:.:.:NOCALL:nocall	0/1:130.73:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:461.73:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:270.6:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:47.6:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:11:FP:lm:d1_5:INDEL:het	15:43846830	43554632
NYGC	HG-002-2x250-b38.recalibrated.haplotypeCalls.vcf.gz	GRCh38	small-variants	INDEL	15	chr15	43846830	43554632	0	FP	CAG	C	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:465.73:FP:lm:d1_5:INDEL:het 	unsure		Simple Repeat. Looks like the GIAB call and ours are the two haplotypes but both VCFs have only one of the variants.	no	yes	hifiasm misses del in homopolymer on opposite haplotype due to highly homozygous region				unsure	yes	dinucleotide repeat (AC).  There appears to be evidence for 2 bp deletion and SNP in adjacent positions.  I'm unsure how the adjacent variants effect this.  																						43846830
Common		GRCh38			15	chr15	43846830	43554632	2	FP	CAG	C	GT:QQ:BD:BK:BI:BVT:BLT	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	CommonFP			no	yes	hifiasm misses del in homopolymer on opposite haplotype due to highly homozygous region													.:.:.:.:.:NOCALL:nocall	0/1:130.73:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:465.73:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:201.6:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:47.6:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:11:FP:lm:d1_5:INDEL:het		43846830
Common		GRCh37			15	chr15	43846832	43554634	0	FP_FN	G	C	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:10.6316:tv:SNP:homalt	1/1:TP:gm:10.6316:tv:SNP:homalt	CommonFP_FN			no	yes	hifiasm misses del in homopolymer on opposite haplotype due to highly homozygous region													1|1:FN:am:.:tv:SNP:homalt	0/1:FP:am:1694.77:tv:SNP:het	1|1:FN:am:.:tv:SNP:homalt	0/1:FP:am:418.77:tv:SNP:het	1|1:FN:am:.:tv:SNP:homalt	0/1:FP:am:30:tv:SNP:het	1|1:TP:gm:5.2:tv:SNP:homalt	1/1:TP:gm:5.2:tv:SNP:homalt	1|1:FN:am:.:tv:SNP:homalt	0/1:FP:am:0:tv:SNP:het	1|1:FN:am:.:tv:SNP:homalt	0/1:FP:am:50:tv:SNP:het	1|1:TP:gm:27:tv:SNP:homalt	1/1:TP:gm:27:tv:SNP:homalt	15:43846832	43554634
Common		GRCh38			15	chr15	43846832	43554634	1906	FP_FN	G	C	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:15.2376:tv:SNP:homalt	1/1:TP:gm:15.2376:tv:SNP:homalt	CommonFP_FN			no	yes	hifiasm misses del in homopolymer on opposite haplotype due to highly homozygous region													1|1:FN:am:.:tv:SNP:homalt	0/1:FP:am:1694.77:tv:SNP:het	1|1:FN:am:.:tv:SNP:homalt	0/1:FP:am:418.77:tv:SNP:het	1|1:FN:am:.:tv:SNP:homalt	0/1:FP:am:30:tv:SNP:het	1|1:TP:gm:5.2:tv:SNP:homalt	1/1:TP:gm:5.2:tv:SNP:homalt	1|1:FN:am:.:tv:SNP:homalt	0/1:FP:am:0:tv:SNP:het	1|1:FN:am:.:tv:SNP:homalt	0/1:FP:am:50:tv:SNP:het	1|1:TP:gm:27:tv:SNP:homalt	1/1:TP:gm:27:tv:SNP:homalt		43846832
Common		GRCh37			15	chr15	43848738	43556540	0	FP_FN	C	CA,CAA	GT:BD:BK:QQ:BI:BVT:BLT	2|2:FN:am:.:i1_5:INDEL:homalt	2/1:FP:am:100:i1_5:INDEL:hetalt	CommonFP_FN			no	yes	hifiasm misses 1bp ins in homopolymer on opposite haplotype due to highly homozygous region													2|2:FN:.:.:i1_5:INDEL:homalt	.:.:.:0:.:NOCALL:nocall	2|2:FN:am:.:i1_5:INDEL:homalt	2/1:FP:am:769.73:i1_5:INDEL:hetalt	2|2:FN:am:.:i1_5:INDEL:homalt	2/1:FP:am:30:i1_5:INDEL:hetalt	2|2:FN:am:.:i1_5:INDEL:homalt	2/1:FP:am:602.1:i1_5:INDEL:hetalt	2|2:TP:gm:0:i1_5:INDEL:homalt	2/1:FP:lm:0:i1_5:INDEL:hetalt	2|2:FN:am:.:i1_5:INDEL:homalt	2/1:FP:am:207.1:i1_5:INDEL:hetalt	2|2:FN:lm:.:i1_5:INDEL:homalt	1/1:FP:lm:15:i1_5:INDEL:homalt	15:43848738	43556540
Common		GRCh38			15	chr15	43848738	43556540	4492	FP_FN	C	CA,CAA	GT:BD:BK:QQ:BI:BVT:BLT	2|2:FN:am:.:i1_5:INDEL:homalt	2/1:FP:am:100:i1_5:INDEL:hetalt	CommonFP_FN			no	yes	hifiasm misses 1bp ins in homopolymer on opposite haplotype due to highly homozygous region													2|2:FN:.:.:i1_5:INDEL:homalt	.:.:.:0:.:NOCALL:nocall	2|2:FN:am:.:i1_5:INDEL:homalt	2/1:FP:am:641.73:i1_5:INDEL:hetalt	2|2:FN:am:.:i1_5:INDEL:homalt	2/1:FP:am:30:i1_5:INDEL:hetalt	2|2:FN:am:.:i1_5:INDEL:homalt	2/1:FP:am:526.1:i1_5:INDEL:hetalt	2|2:TP:gm:0:i1_5:INDEL:homalt	2/1:FP:lm:0:i1_5:INDEL:hetalt	2|2:FN:am:.:i1_5:INDEL:homalt	2/1:FP:am:207.42:i1_5:INDEL:hetalt	2|2:FN:lm:.:i1_5:INDEL:homalt	1/1:FP:lm:15:i1_5:INDEL:homalt		43848738
ITER	ITERteam_small-variation_GRCh37_ILMN-PB-ONT.vcf.gz	GRCh37	small-variants	INDEL	15	chr15	43853230	43561032	207	FP	A	AT	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	1/1:17.7:FP:am:i1_5:INDEL:homalt	Yes	No																															15:43853230	43561032
CMH_DRAGEN_3.6.3	NA24385.hard-filtered.vcf.gz	GRCh37	small-variants	INDEL	15	chr15	43853437	43561239	889	FN	GA	G	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:.:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	yes	no																															15:43853437	43561239
NYGC	HG-002-2x250-b38.recalibrated.haplotypeCalls.vcf.gz	GRCh38	small-variants	SNP	15	chr15	43854326	43562128	339	FN	G	A	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0 	yes	no								skip																								43854326
NYGC	HG-002-2x250-b38.recalibrated.haplotypeCalls.vcf.gz	GRCh38	small-variants	SNP	15	chr15	43854665	43562467	16280	FN	A	C	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0 	yes	no								skip																								43854665
Common		GRCh37			15	chr15	43870945	43578747	0	FN	GC	G	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no	yes	looks like hifiasm consensus indel error not in homopolymer since no evidence across techs													0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	15:43870945	43578747
Common		GRCh38			15	chr15	43870945	43578747	115	FN	GC	G	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no	yes	looks like hifiasm consensus indel error not in homopolymer since no evidence across techs													0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0		43870945
CMH_DRAGEN_3.6.3	NA24385.hard-filtered.vcf.gz	GRCh37	small-variants	SNP	15	chr15	43871060	43578862	521	FP	A	C	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:26.13:FP:.:tv:SNP:het	yes	no	in selfchain. Low quality call in query (17)																														15:43871060	43578862
Common		GRCh37			15	chr15	43871581	43579383	1138	FP	TACACACACAC	TACACACACACAC,T	GT:QQ:BD:BK:BI:BVT:BLT	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	CommonFP			unsure	unsure	while most HiFi reads support large del in diTR, a couple support the 2bp ins that many illumina and 10x reads support.													.:.:.:.:.:NOCALL:nocall	0/2:1808.73:FP:lm:d6_15:INDEL:het	.:.:.:.:.:NOCALL:nocall	1/1:492.73:FP:lm:i1_5:INDEL:homalt	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	1/1:0:FP:lm:i1_5:INDEL:homalt	.:.:.:.:.:NOCALL:nocall	1/1:70.31:FP:lm:i1_5:INDEL:homalt	.:.:.:.:.:NOCALL:nocall	1/1:13:FP:lm:i1_5:INDEL:homalt	15:43871581	43579383
NYGC	HG-002-2x250-b37.recalibrated.haplotypeCalls.vcf.gz	GRCh37	small-variants	SNP	15	chr15	43872719	43580521	0	FP_FN	G	C	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:tv:SNP:homalt	0/1:FP:am:1200.77:tv:SNP:het 	unsure	yes	There is clear evidence for the reference allele in the high coverage Illumina data and some evidence for it in the Pacbio CCS and ONT data.	yes	No	Illumina and 10x support het but have higher than normal coverage so likely due to mismapped reads, since HiFi and ONT support homvar																											15:43872719	43580521
DNAnexus	GRCh38_HG002_WGS_union.vcf.gz	GRCh38	small-variants	SNP	15	chr15	43872719	43580521	0	FP_FN	G	C	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:tv:SNP:homalt	0/1:FP:am:0:tv:SNP:het 	no	yes	Illumina, 10x and ONT indicate het calls while Pacbio shows hom-ref.	yes	No	Illumina and 10x support het but have higher than normal coverage so likely due to mismapped reads, since HiFi and ONT support homvar				unsure	yes	segdup. missing haplotype for HiiFi but HP present support benchmark HOM. Nearby variant at (435805696) does nIot appear to have correlation with this variant possibly implying similar sequence duplication somewhere else.  ILMN (high coverage) and 10X (normalish) support presence of ALT (C) however are HET. given this is a segdup and 1) Hifii is not HP separated and 2) ILMN has high coverage I'm unsure. Some support for variant however no evidence has ideal representation.																						43872719
BCM-HGSC_xAtlas	HG002.GRCh38.60x.1_merged.vcf.gz	GRCh38	small-variants	SNP	15	chr15	43872719	43580521	6915959	FP_FN	G	C	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:tv:SNP:homalt	0/1:FP:am:23:tv:SNP:het 	Yes	No		yes	No	Illumina and 10x support het but have higher than normal coverage so likely due to mismapped reads, since HiFi and ONT support homvar				skip																								43872719
Common		GRCh37			15	chr15	50788677	50496480	0	FP	TA	T	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:lm:d1_5:INDEL:het	CommonFP			no	yes	hifiasm misses del in long homopolymer opposite 2bp ins, which is clear in Illumina and noisy in HiFi													.:.:.:.:.:NOCALL:nocall	0/1:132.73:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:228.73:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:311.06:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	1/1:0:FP:lm:d1_5:INDEL:homalt	.:.:.:.:.:NOCALL:nocall	0/1:149.76:FP:lm:d1_5:INDEL:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	15:50788677	50496480
ITER	ITERteam_small-variation_GRCh38_ILMN-PB-ONT.vcf.gz	GRCh38	small-variants	INDEL	15	chr15	50788677	50496480	0	FP	TA	T	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:213.06:FP:lm:d1_5:INDEL:het	Unsure	Unsure	We both called a 2nt insertion but in a different manner (truth as T:TAA and query as TA:TAAA). But, truth did not call this deletion (TA:T) that is well supported by ILMN and 10x in truth and ILMN in query.	no	yes	hifiasm misses del in long homopolymer opposite 2bp ins, which is clear in Illumina and noisy in HiFi						having trouble with deletions, similar to row 96																						50788677
Common		GRCh38			15	chr15	50788677	50496480	-50201417	FP	TA	T	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:lm:d1_5:INDEL:het	CommonFP			no	yes	hifiasm misses del in long homopolymer opposite 2bp ins, which is clear in Illumina and noisy in HiFi													.:.:.:.:.:NOCALL:nocall	0/1:132.73:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:210.73:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:213.06:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	1/1:0:FP:lm:d1_5:INDEL:homalt	.:.:.:.:.:NOCALL:nocall	0/1:149.87:FP:lm:d1_5:INDEL:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.		50788677
Common		GRCh37			16	chr16	345063	295063	0	FN	C	CA	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no	yes	benchmark error due to noisy HiFi in homopolymer													1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	16:345063	295063
Common		GRCh38			16	chr16	345063	295063	31308	FN	C	CA	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no	yes	benchmark error due to noisy HiFi in homopolymer													1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0		345063
Common		GRCh37			16	chr16	376371	326371	1	FN	AAATATAT	A	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:lm:d6_15:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no	yes	benchmark has 7bp del instead of 6bp del in adjacent homopolymer/diTR													1|0:FN:.:d6_15:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:lm:d6_15:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:lm:d6_15:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:d6_15:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:lm:d6_15:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:lm:d6_15:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:lm:d6_15:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	16:376371	326371
BCM-HGSC_xAtlas	HG002.hs37d5.60x.1_merged.vcf.gz	GRCh37	small-variants	INDEL	16	chr16	376372	326372	0	FP	AATATAT	A	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:7:FP:lm:d6_15:INDEL:het 	Yes	No		no	yes	benchmark has 7bp del instead of 6bp del in adjacent homopolymer/diTR																											16:376372	326372
Common		GRCh37			16	chr16	376372	326372	585248	FP	AATATAT	A	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:lm:d6_15:INDEL:het	CommonFP			no	yes	benchmark has 7bp del instead of 6bp del in adjacent homopolymer/diTR													./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:417.77:FP:lm:d6_15:INDEL:het	.:.:.:.:.:NOCALL:nocall	1/1:30:FP:lm:d6_15:INDEL:homalt	.:.:.:.:.:NOCALL:nocall	0/1:406.08:TP:gm:d6_15:INDEL:het	.:.:.:.:.:NOCALL:nocall	1/1:0:FP:lm:d6_15:INDEL:homalt	.:.:.:.:.:NOCALL:nocall	0/1:74.58:FP:lm:d6_15:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:7:FP:lm:d6_15:INDEL:het	16:376372	326372
Common		GRCh37			16	chr16	961620	911620	0	FN	T	TG	GT:BD:BK:BI:BVT:BLT:QQ	0|1:TP:gm:i1_5:INDEL:het:18.9709	0/1:TP:gm:i1_5:INDEL:het:18.9709	CommonFN			unsure		benchmark likely correct but difficult to know for sure since it's a noisy homopolymer in a long tandem repeat													0|1:TP:gm:i1_5:INDEL:het:36.73	0/1:TP:gm:i1_5:INDEL:het:36.73	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:TP:gm:i1_5:INDEL:het:49.99	0/1:TP:gm:i1_5:INDEL:het:49.99	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	16:961620	911620
Common		GRCh38			16	chr16	961620	911620	40483	FN	T	TG	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			unsure		benchmark likely correct but difficult to know for sure since it's a noisy homopolymer in a long tandem repeat													0|1:TP:gm:i1_5:INDEL:het:36.73	0/1:TP:gm:i1_5:INDEL:het:36.73	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:TP:gm:i1_5:INDEL:het:37.11	0/1:TP:gm:i1_5:INDEL:het:37.11	0|1:FN:lm:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:TP:gm:i1_5:INDEL:het:49.99	0/1:TP:gm:i1_5:INDEL:het:49.99	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0		961620
CMH_DRAGEN_3.6.3	NA24385.hard-filtered.vcf.gz	GRCh37	small-variants	SNP	16	chr16	1002103	952103	400864	FN	G	A	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	yes	no																															16:1002103	952103
Common		GRCh37			16	chr16	1402968	1352967	0	FP_FN	A	AT	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:100:i1_5:INDEL:het	CommonFP_FN			no	yes	likely hifiasm error in due to noisy HiFi in long homopolymer													1|1:FN:.:.:i1_5:INDEL:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:113.73:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:30:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:171.64:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:0:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:50:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:6:i1_5:INDEL:het	16:1402968	1352967
Common		GRCh38			16	chr16	1402968	1352967	48560	FP_FN	A	AT	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:100:i1_5:INDEL:het	CommonFP_FN			no	yes	likely hifiasm error in due to noisy HiFi in long homopolymer													1|1:FN:.:.:i1_5:INDEL:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:118.73:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:30:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:178.64:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:0:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:50:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:6:i1_5:INDEL:het		1402968
Common		GRCh37			16	chr16	1451528	1401527	70842	FN	G	GC	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:lm:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no	yes	likely hifiasm error in C homopolymer due to noisy HiFi													0|1:TP:gm:i1_5:INDEL:het:297.73	0/1:TP:gm:i1_5:INDEL:het:297.73	0|1:FN:lm:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	16:1451528	1401527
DNAnexus	hs37d5_HG002_WGS_union.vcf.gz	GRCh37	small-variants	SNP	16	chr16	1522370	1472369	203	FN	T	C	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	yes	no																															16:1522370	1472369
DNAnexus	GRCh38_HG002_WGS_union.vcf.gz	GRCh38	small-variants	SNP	16	chr16	1522573	1472572	902	FN	C	T	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0 	yes	no								skip																								1522573
BCM-HGSC_xAtlas	HG002.GRCh38.60x.1_merged.vcf.gz	GRCh38	small-variants	SNP	16	chr16	1523475	1473474	630252	FN	A	C	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:lm:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0 	Yes	No								skip																								1523475
PacBio_gatk4	gatk4hc_HG002_15kb_20kb_52X_SequelII.vcf.gz	GRCh37	small-variants	SNP	16	chr16	2153727	2103726	0	FP	C	T	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:79.77:FP:.:ti:SNP:het	unsure	unsure	supported by all reads, not supported by assembly	no	yes	hifiasm misses SNV due to highly homozygous region																											16:2153727	2103726
Common		GRCh37			16	chr16	2153727	2103726	0	FP	C	T	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:.:ti:SNP:het	CommonFP			no	yes	hifiasm misses SNV due to highly homozygous region													.:.:.:.:.:NOCALL:nocall	0/1:79.77:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:661.77:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:423.6:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:46.6:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:35:FP:.:ti:SNP:het	16:2153727	2103726
Common		GRCh38			16	chr16	2153727	2103726	443111	FP	C	T	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:.:ti:SNP:het	CommonFP			no	yes	hifiasm misses SNV due to highly homozygous region													.:.:.:.:.:NOCALL:nocall	0/1:79.77:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:732.77:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:451.6:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:46.6:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:35:FP:.:ti:SNP:het		2153727
PacBio_gatk4	gatk4hc_HG002_15kb_20kb_52X_SequelII.vcf.gz	GRCh37	small-variants	SNP	16	chr16	2596838	2546837	3151	FP	G	C	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:141.77:FP:.:tv:SNP:het	yes	no																															16:2596838	2546837
PacBio_gatk4	gatk4hc_HG002_15kb_20kb_52X_SequelII.vcf.gz	GRCh37	small-variants	SNP	16	chr16	2599989	2549988	7741	FP	A	G	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:222.77:FP:.:ti:SNP:het	yes	no																															16:2599989	2549988
Common		GRCh37			16	chr16	2607730	2557729	0	FP	C	T	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:23.2841:FP:.:ti:SNP:het	CommonFP			yes	no	interesting region in PDPK1 that seems to have mismapped HiFi reads since the reads map equally well elsewhere, there are 3 haplotypes, and only a few relatively short ONT reads support the variants. The reads seem to be mismapping rather than being a duplication since one haplotype is missing from the other copy of the segdup and there is a 2kb del in HG002 there													.:.:.:.:.:NOCALL:nocall	0/1:443.77:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:405.77:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:.:ti:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:25.07:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:28:FP:.:ti:SNP:het	16:2607730	2557729
Common		GRCh38			16	chr16	2607730	2557729	271	FP	C	T	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:24.0936:FP:.:ti:SNP:het	CommonFP			yes	no	interesting region in PDPK1 that seems to have mismapped HiFi reads since the reads map equally well elsewhere, there are 3 haplotypes, and only a few relatively short ONT reads support the variants. The reads seem to be mismapping rather than being a duplication since one haplotype is missing from the other copy of the segdup and there is a 2kb del in HG002 there													.:.:.:.:.:NOCALL:nocall	0/1:442.77:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:412.77:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:.:ti:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:25.07:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:28:FP:.:ti:SNP:het		2607730
Common		GRCh37			16	chr16	2608001	2558000	0	FP	G	A	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:23.2841:FP:.:ti:SNP:het	CommonFP			yes	no	interesting region in PDPK1 that seems to have mismapped HiFi reads since the reads map equally well elsewhere, there are 3 haplotypes, and only a few relatively short ONT reads support the variants. The reads seem to be mismapping rather than being a duplication since one haplotype is missing from the other copy of the segdup and there is a 2kb del in HG002 there													.:.:.:.:.:NOCALL:nocall	0/1:453.77:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:329.77:FP:.:ti:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:24.41:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:15:FP:.:ti:SNP:het	16:2608001	2558000
Common		GRCh38			16	chr16	2608001	2558000	538	FP	G	A	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:8.7205:FP:.:ti:SNP:het	CommonFP			yes	no	interesting region in PDPK1 that seems to have mismapped HiFi reads since the reads map equally well elsewhere, there are 3 haplotypes, and only a few relatively short ONT reads support the variants. The reads seem to be mismapping rather than being a duplication since one haplotype is missing from the other copy of the segdup and there is a 2kb del in HG002 there													.:.:.:.:.:NOCALL:nocall	0/1:453.77:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:294.77:FP:.:ti:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:24.41:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:15:FP:.:ti:SNP:het		2608001
PacBio_gatk4	gatk4hc_HG002_15kb_20kb_52X_SequelII.vcf.gz	GRCh37	small-variants	SNP	16	chr16	2608539	2558538	6614	FP	C	T	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:359.77:FP:.:ti:SNP:het	no	yes	supported by all reads, not supported by assembly	yes	no	interesting region in PDPK1 that seems to have mismapped HiFi reads since the reads map equally well elsewhere, there are 3 haplotypes, and only a few relatively short ONT reads support the variants. The reads seem to be mismapping rather than being a duplication since one haplotype is missing from the other copy of the segdup and there is a 2kb del in HG002 there																											16:2608539	2558538
PacBio_gatk4	gatk4hc_HG002_15kb_20kb_52X_SequelII.vcf.gz	GRCh37	small-variants	SNP	16	chr16	2615153	2565152	4393	FP_FN	C	T	GT:BD:BK:QQ:BI:BVT:BLT	0|1:FN:am:.:ti:SNP:het	1/1:FP:am:195.9:ti:SNP:homalt	yes	no		yes	no	interesting region in PDPK1 that seems to have mismapped HiFi reads since the reads map equally well elsewhere, there are 3 haplotypes, and only a few relatively short ONT reads support the variants. The reads seem to be mismapping rather than being a duplication since one haplotype is missing from the other copy of the segdup and there is a 2kb del in HG002 there																											16:2615153	2565152
Common		GRCh37			16	chr16	2619546	2569545	0	FN	G	A	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	error in short reads due to difficulty mapping in segdup													1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:ti:SNP:het:26.2	0/1:TP:gm:ti:SNP:het:26.2	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	16:2619546	2569545
Common		GRCh38			16	chr16	2619546	2569545	2392	FN	G	A	GT:BD:BK:QQ:BI:BVT:BLT	1|0:TP:gm:12.5093:ti:SNP:het	0/1:TP:gm:12.5093:ti:SNP:het	CommonFN			yes	no	error in short reads due to difficulty mapping in segdup													1|0:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	1|0:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	1|0:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	1|0:TP:gm:13.6:ti:SNP:het	0/1:TP:gm:13.6:ti:SNP:het	1|0:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	1|0:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	1|0:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall		2619546
Common		GRCh37			16	chr16	2621938	2571937	0	FN	C	CA	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			unsure	unsure	benchmark may be correct, but hard to tell in very long homopolymer with no illumina reads mapping and noisy other techs													0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	16:2621938	2571937
PacBio_gatk4	gatk4hc_HG002_15kb_20kb_53X_SequelII.vcf.gz	GRCh38	small-variants	INDEL	16	chr16	2621938	2571937	0	FN	C	CA	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	yes	no		unsure	unsure	benchmark may be correct, but hard to tell in very long homopolymer with no illumina reads mapping and noisy other techs				skip																								2621938
Common		GRCh38			16	chr16	2621938	2571937	4103	FN	C	CA	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			unsure		benchmark may be correct, but hard to tell in very long homopolymer with no illumina reads mapping and noisy other techs													0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0		2621938
NCBI	HG002_grch38_dipcall.vcf.gz	GRCh38	small-variants	SNP	16	chr16	2626041	2576040	7000	FP	A	G	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	1/1:30:FP:.:ti:SNP:homalt	yes	no	segdup region	yes	no	no support for variant in segdup				skip																								2626041
ITER	ITERteam_small-variation_GRCh37_ILMN-PB-ONT.vcf.gz	GRCh37	small-variants	INDEL	16	chr16	2633041	2583040	16702	FN	AT	A	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	Unsure	Unsure	Bad support in both truth (except 10X reads) and query.	unsure	unsure	benchmark appears to be correct based on average of 10x and HiFi reads on each haplotype, but lack of illumina coverage makes it hard to know for sure in long homopolymer																											16:2633041	2583040
Common		GRCh37			16	chr16	2649743	2599742	16212770	FP	CGTCCTGTGTCTCCAT	C	GT:QQ:BD:BK:BI:BVT:BLT	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	CommonFP			yes	no	error in short reads due to difficulty mapping in segdup													./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:769.73:FP:.:d6_15:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:.:d6_15:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:772.6:FP:.:d6_15:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:.:d6_15:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:30.35:FP:.:d6_15:INDEL:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	16:2649743	2599742
NCBI	HG002_grch37_dipcall.vcf.gz	GRCh37	small-variants	SNP	16	chr16	18823834	18812512	985	FN	T	C	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	yes	no	no repeat here																														16:18823834	18812512
NCBI	HG002_grch37_dipcall.vcf.gz	GRCh37	small-variants	SNP	16	chr16	18824819	18813497	5282	FN	G	A	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	yes	no	repeat region																														16:18824819	18813497
NCBI	HG002_grch37_dipcall.vcf.gz	GRCh37	small-variants	SNP	16	chr16	18830101	18818779	250	FN	C	T	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	yes	no	no repeat here																														16:18830101	18818779
NCBI	HG002_grch37_dipcall.vcf.gz	GRCh37	small-variants	SNP	16	chr16	18830351	18819029	57635	FN	C	G	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	yes	no	repeat region																														16:18830351	18819029
CMH_DRAGEN_3.6.3	NA24385.hard-filtered.vcf.gz	GRCh37	small-variants	INDEL	16	chr16	18887986	18876664	4057	FP_FN	G	GT	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:49.54:i1_5:INDEL:het	yes	no																															16:18887986	18876664
Common		GRCh37			16	chr16	18892043	18880721	0	FP_FN	A	AGG,AGGG,AGGGG	GT:BD:BK:QQ:BI:BVT:BLT	2|3:FN:am:.:i1_5:INDEL:hetalt	2/1:FP:am:100:i1_5:INDEL:hetalt	CommonFP_FN			no		3bp/2bp ins in adjacent homopolymers supported clearly by illumina, and other techs are noisy													2|3:FN:am:.:i1_5:INDEL:hetalt	2/2:FP:am:1319.73:i1_5:INDEL:homalt	2|3:FN:am:.:i1_5:INDEL:hetalt	2/2:FP:am:278.73:i1_5:INDEL:homalt	2|3:FN:.:.:i1_5:INDEL:hetalt	.:.:.:0:.:NOCALL:nocall	2|3:FN:.:.:i1_5:INDEL:hetalt	.:.:.:0:.:NOCALL:nocall	.:.:.:.:.:NOCALL:nocall	2/2:FP:am:0:i1_5:INDEL:homalt	2|3:FN:lm:.:i1_5:INDEL:hetalt	1/1:FP:lm:57.73:i1_5:INDEL:homalt	2|3:FN:lm:.:i1_5:INDEL:hetalt	1/1:FP:lm:15:i1_5:INDEL:homalt	16:18892043	18880721
Common		GRCh38			16	chr16	18892043	18880721	6795	FP_FN	A	AGG,AGGG,AGGGG	GT:BD:BK:BI:QQ:BVT:BLT	2|3:FN:am:i1_5:.:INDEL:hetalt	2/1:FP:am:i1_5:100:INDEL:hetalt	CommonFP_FN			no		3bp/2bp ins in adjacent homopolymers supported clearly by illumina, and other techs are noisy													2|3:FN:am:i1_5:.:INDEL:hetalt	2/2:FP:am:i1_5:1319.73:INDEL:homalt	2|3:FN:am:i1_5:.:INDEL:hetalt	2/2:FP:am:i1_5:237.73:INDEL:homalt	2|3:FN:am:i1_5:.:INDEL:hetalt	2/2:FP:am:i1_5:30:INDEL:homalt	2|3:FN:am:i1_5:.:INDEL:hetalt	2/2:FP:am:i1_5:65.84:INDEL:homalt	.:.:.:.:.:NOCALL:nocall	2/2:FP:am:i1_5:0:INDEL:homalt	2|3:FN:lm:i1_5:.:INDEL:hetalt	1/1:FP:lm:i1_5:57.5:INDEL:homalt	2|3:FN:lm:i1_5:.:INDEL:hetalt	1/1:FP:lm:i1_5:15:INDEL:homalt		18892043
NCBI	HG002_grch37_dipcall.vcf.gz	GRCh37	small-variants	INDEL	16	chr16	18898838	18887516	962	FN	C	CTTTGTTTTTT,CTTTGTTTTTTTTTTTT	GT:BD:BK:BI:BVT:BLT:QQ	1|2:FN:.:i16_plus,i6_15:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:0	yes	no	evidence for 10-18bps INS; segdup region																														16:18898838	18887516
ITER	ITERteam_small-variation_GRCh38_ILMN-PB-ONT.vcf.gz	GRCh38	small-variants	INDEL	16	chr16	18899800	18888478	27591	FN	CT	C	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	Unsure	Unsure	Mainly supported by ILMN and 10x reads in truth and by ILMN and PacBio in query (long reads support longer deletions). 	yes	no	homopolymer supported by illumina, haplotype-partitioned in 10x, though HiFi is noisy and not haplotype partitioned				unsure	yes	homopolymer in Segdup. 10X and ILMN support HET.  Hifi also supports HET but not HP separated.  I would say call is correct however have reservation because coverage at this position is lower for all																						18899800
NCBI	HG002_grch37_dipcall.vcf.gz	GRCh37	small-variants	INDEL	16	chr16	18927391	18916069	0	FN	C	CAA	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	yes	no	segdup region	yes	no	homopolymer supported by illumina, haplotype-partitioned in 10x, though HiFi is noisy and not haplotype partitioned																											16:18927391	18916069
Common		GRCh37			16	chr16	18927391	18916069	9943799	FN	C	CAA	GT:BD:BK:BI:BVT:BLT:QQ	0|1:TP:gm:i1_5:INDEL:het:100	0/1:TP:gm:i1_5:INDEL:het:100	CommonFN			yes	no	homopolymer supported by illumina, haplotype-partitioned in 10x, though HiFi is noisy and not haplotype partitioned													0|1:TP:gm:i1_5:INDEL:het:101.73	0/1:TP:gm:i1_5:INDEL:het:101.73	0|1:FN:lm:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:TP:gm:i1_5:INDEL:het:50	0/1:TP:gm:i1_5:INDEL:het:50	0|1:FN:lm:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	16:18927391	18916069
NCBI	HG002_grch37_dipcall.vcf.gz	GRCh37	small-variants	INDEL	16	chr16	28871189	28859868	0	FN	A	AC	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	yes	no	most evidence for 1-2 CC INS here; but ONT for DEL here	no	yes	Since illumina has no evidence for the ins, it seems unlikely to be a true variant, though illumina does have systematic errors in the C homopolymer																											16:28871189	28859868
Common		GRCh37			16	chr16	28871189	28859868	0	FN	A	AC	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no	yes	Since illumina has no evidence for the ins, it seems unlikely to be a true variant, though illumina does have systematic errors in the C homopolymer													0|1:TP:gm:i1_5:INDEL:het:120.73	0/1:TP:gm:i1_5:INDEL:het:120.73	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	16:28871189	28859868
NCBI	HG002_grch38_dipcall.vcf.gz	GRCh38	small-variants	INDEL	16	chr16	28871189	28859868	0	FN	A	AC	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	unsure	unsure	only PB support benchmark; ONT for 6-7 Cs here with good mapping ; no segdup/repeat here	no	yes	Since illumina has no evidence for the ins, it seems unlikely to be a true variant, though illumina does have systematic errors in the C homopolymer																												28871189
Common		GRCh38			16	chr16	28871189	28859868	1891857	FN	A	AC	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no	yes	Since illumina has no evidence for the ins, it seems unlikely to be a true variant, though illumina does have systematic errors in the C homopolymer													0|1:TP:gm:i1_5:INDEL:het:120.73	0/1:TP:gm:i1_5:INDEL:het:120.73	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0		28871189
Common		GRCh37			16	chr16	30763046	30751725	0	FP_FN	C	CT	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:100:i1_5:INDEL:het	CommonFP_FN			no	yes	missed ins in highly homozygous region not in homopolymer													1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:667.73:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:820.73:i1_5:INDEL:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:644.64:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:0:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:48.13:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:14:i1_5:INDEL:het	16:30763046	30751725
Common		GRCh38			16	chr16	30763046	30751725	40083140	FP_FN	C	CT	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:100:i1_5:INDEL:het	CommonFP_FN			no	yes	missed ins in highly homozygous region not in homopolymer													1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:667.73:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:822.73:i1_5:INDEL:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:496.64:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:0:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:48.13:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:14:i1_5:INDEL:het		30763046
Common		GRCh37			16	chr16	70868768	70834865	0	FP_FN	C	CAT	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:100:i1_5:INDEL:het	CommonFP_FN			no	yes	hifiasm misses ref haplotype for indel in TR in highly homozygous region													1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:867.73:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:747.73:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:30:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:1058.64:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:0:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:50:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:12:i1_5:INDEL:het	16:70868768	70834865
CMH_DRAGEN_3.6.3	NA24385.hard-filtered.vcf.gz	GRCh38	small-variants	INDEL	16	chr16	70868768	70834865	0	FP_FN	C	CAT	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:50:i1_5:INDEL:het	unsure	unsure	Conflicting evidences exist. In segdup. PacBio is not phased	no	yes	hifiasm misses ref haplotype for indel in TR in highly homozygous region																												70868768
Roche	RN_HG002_Illumina_PacBio_Oxford.vcf.gz	GRCh38	small-variants	INDEL	16	chr16	70868768	70834865	0	FP_FN	C	CAT	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:100:i1_5:INDEL:het 	no	yes	Seems HET from all technologies	no	yes	hifiasm misses ref haplotype for indel in TR in highly homozygous region				no	yes	TR in Segdup.. ALT appears correct however evidence of HET 0/1. Hifi missing second HP but evidence for REF/ALT.  ILMN also has evidence for REF/ALT																						70868768
Common		GRCh38			16	chr16	70868768	70834865	8181	FP_FN	C	CAT	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:100:i1_5:INDEL:het	CommonFP_FN			no	yes	hifiasm misses ref haplotype for indel in TR in highly homozygous region													1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:867.73:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:729.73:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:30:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:247.64:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:0:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:50:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:12:i1_5:INDEL:het		70868768
Common		GRCh37			16	chr16	70876949	70843046	0	FP_FN	C	CT	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:100:i1_5:INDEL:het	CommonFP_FN			no	yes	hifiasm misses ref haplotype for indel in homopolymer in highly homozygous region													1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:782.73:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:281.73:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:30:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:637.64:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:0:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:44.75:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:16:i1_5:INDEL:het	16:70876949	70843046
Common		GRCh38			16	chr16	70876949	70843046	12761	FP_FN	C	CT	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:100:i1_5:INDEL:het	CommonFP_FN			no	yes	hifiasm misses ref haplotype for indel in homopolymer in highly homozygous region													1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:782.73:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:281.73:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:30:i1_5:INDEL:het	1|1:FN:.:.:i1_5:INDEL:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:0:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:44.35:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:16:i1_5:INDEL:het		70876949
Common		GRCh38			16	chr16	70889710	70855807	20376	FP	A	G	GT:QQ:BD:BK:BI:BVT:BLT	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	CommonFP			yes	no	mapping error from short reads													./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:508.77:FP:.:ti:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:298.6:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:30.58:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:24:FP:.:ti:SNP:het		70889710
Common		GRCh37			16	chr16	70910086	70876183	0	FP	A	AT	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:.:i1_5:INDEL:het	CommonFP			no	yes	hifiasm misses variant haplotype for indel in homopolymer in highly homozygous region													.:.:.:.:.:NOCALL:nocall	0/1:160.73:FP:.:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:257.73:FP:.:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:.:i1_5:INDEL:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:.:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:40.38:FP:.:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:15:FP:.:i1_5:INDEL:het	16:70910086	70876183
Roche	RN_HG002_Illumina_PacBio_Oxford.vcf.gz	GRCh38	small-variants	INDEL	16	chr16	70910086	70876183	0	FP	A	AT	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:.:i1_5:INDEL:het 	unsure	unsure	Seems real from Illumina and PacBio, but it is also a large (>300K segdup) so it may be not from this region. The mapq is also  high which makes it more likely to be a true variant	no	yes	hifiasm misses variant haplotype for indel in homopolymer in highly homozygous region				no	yes	homopolymer in Segdup. 10X and ILMN support HET.  Hifi also supports HET but not HP separated.  coverage reasonable for all																						70910086
Common		GRCh38			16	chr16	70910086	70876183	16992	FP	A	AT	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:.:i1_5:INDEL:het	CommonFP			no	yes	hifiasm misses variant haplotype for indel in homopolymer in highly homozygous region													.:.:.:.:.:NOCALL:nocall	0/1:160.73:FP:.:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:292.73:FP:.:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:.:i1_5:INDEL:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:.:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:40.38:FP:.:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:15:FP:.:i1_5:INDEL:het		70910086
Common		GRCh37			16	chr16	70927078	70893175	0	FP	C	T	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:.:ti:SNP:het	CommonFP			no	yes	hifiasm misses ref haplotype for SNV in highly homozygous region													.:.:.:.:.:NOCALL:nocall	0/1:1049.77:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:770.77:FP:.:ti:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:572.6:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:34.07:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:24:FP:.:ti:SNP:het	16:70927078	70893175
Common		GRCh38			16	chr16	70927078	70893175	7542	FP	C	T	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:.:ti:SNP:het	CommonFP			no	yes	hifiasm misses ref haplotype for SNV in highly homozygous region													.:.:.:.:.:NOCALL:nocall	0/1:1049.77:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:777.77:FP:.:ti:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:458.13:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:33.2:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:28:FP:.:ti:SNP:het		70927078
Common		GRCh37			16	chr16	70934620	70900717	0	FP_FN	G	GTTCA	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:100:i1_5:INDEL:het	CommonFP_FN			no	yes	hifiasm misses ref haplotype in highly homozygous region													1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:1438.73:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:1008.73:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:30:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:281.64:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:0:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:45.3:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:8:i1_5:INDEL:het	16:70934620	70900717
Common		GRCh38			16	chr16	70934620	70900717	197	FP_FN	G	GTTCA	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:100:i1_5:INDEL:het	CommonFP_FN			no	yes	hifiasm misses ref haplotype in highly homozygous region													1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:1438.73:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:1011.73:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:30:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:1035.64:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:0:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:41.13:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:9:i1_5:INDEL:het		70934620
Common		GRCh37			16	chr16	70934817	70900914	0	FP	CTG	C,CTGTG	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/2:100:FP:.:i1_5:INDEL:het	CommonFP			unsure	unsure	some illumina reads have del but low MQ and some HiFi reads have ins in TR but are noisy													.:.:.:.:.:NOCALL:nocall	0/2:94.73:FP:.:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:487.73:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/2:30:FP:.:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:198.6:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:55.03:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:11:FP:.:d1_5:INDEL:het	16:70934817	70900914
Roche	RN_HG002_Illumina_PacBio_Oxford.vcf.gz	GRCh38	small-variants	INDEL	16	chr16	70934817	70900914	0	FP	C	CTG	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:.:i1_5:INDEL:het 	unsure	unsure	Seems real from PacBio and ONT, but it is also a large (>300K segdup) so it may be not from this region. The mapq is also  high which makes it more likely to be a true variant	unsure	unsure	some illumina reads have del but low MQ and some HiFi reads have ins in TR but are noisy				unsure	see note	TR in Segdup. ILMN has mix of REF and deletion, not inserstion, and coverage is low. Hifi supports insertion but no HP separated. 10X is HP separated but less support for ins.  Nothing really agrees.  nearby variant (70900914) in query disagrees with benchmark variant. It looks as thought their call migth be correct, look more like HET than HOM. 																						70934817
Common		GRCh38			16	chr16	70934817	70900914	1880	FP	CTG	CTGTG,C	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:.:i1_5:INDEL:het	CommonFP			unsure	unsure	some illumina reads have del but low MQ and some HiFi reads have ins in TR but are noisy													.:.:.:.:.:NOCALL:nocall	0/1:94.73:FP:.:i1_5:INDEL:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:.:i1_5:INDEL:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/2:0:FP:.:d1_5:INDEL:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/2:12:FP:.:d1_5:INDEL:het		70934817
Common		GRCh37			16	chr16	70936697	70902794	0	FP_FN	AATATATATATATAT	A	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:d6_15:INDEL:homalt	0/1:FP:am:100:d6_15:INDEL:het	CommonFP_FN			no		illumina reads seem to clearly support 13bp and 14bp del aligned to different locations of adjacent TR and homopolymer, and 10x is partly sepparated by haplotype and HiFi is noisy, so benchmark is likely wrong													1|1:FN:am:.:d6_15:INDEL:homalt	0/1:FP:am:208.73:d6_15:INDEL:het	1|1:FN:am:.:d6_15:INDEL:homalt	0/1:FP:am:196.73:d6_15:INDEL:het	1|1:FN:am:.:d6_15:INDEL:homalt	0/1:FP:am:30:d6_15:INDEL:het	1|1:FN:lm:.:d6_15:INDEL:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:d6_15:INDEL:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:am:.:d6_15:INDEL:homalt	0/1:FP:am:44.14:d6_15:INDEL:het	1|1:FN:am:.:d6_15:INDEL:homalt	0/1:FP:am:11:d6_15:INDEL:het	16:70936697	70902794
Common		GRCh38			16	chr16	70936697	70902794	15	FP_FN	AATATATATATATAT	A	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:d6_15:INDEL:homalt	0/1:FP:am:100:d6_15:INDEL:het	CommonFP_FN			no		illumina reads seem to clearly support 13bp and 14bp del aligned to different locations of adjacent TR and homopolymer, and 10x is partly sepparated by haplotype and HiFi is noisy, so benchmark is likely wrong													1|1:FN:am:.:d6_15:INDEL:homalt	0/1:FP:am:208.73:d6_15:INDEL:het	1|1:FN:am:.:d6_15:INDEL:homalt	0/1:FP:am:69.73:d6_15:INDEL:het	1|1:FN:am:.:d6_15:INDEL:homalt	0/1:FP:am:30:d6_15:INDEL:het	1|1:FN:am:.:d6_15:INDEL:homalt	0/1:FP:am:171.6:d6_15:INDEL:het	1|1:FN:.:.:d6_15:INDEL:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:am:.:d6_15:INDEL:homalt	0/1:FP:am:43.4:d6_15:INDEL:het	1|1:FN:am:.:d6_15:INDEL:homalt	0/1:FP:am:12:d6_15:INDEL:het		70936697
Common		GRCh37			16	chr16	70936712	70902809	0	FP	ATATATATATATAT	A	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:lm:d6_15:INDEL:het	CommonFP			no		illumina reads seem to clearly support 13bp and 14bp del aligned to different locations of adjacent TR and homopolymer, and 10x is partly sepparated by haplotype and HiFi is noisy, so benchmark is likely wrong													.:.:.:.:.:NOCALL:nocall	0/1:402.73:FP:lm:d6_15:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:202.73:FP:lm:d6_15:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:lm:d6_15:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:372.6:FP:lm:d6_15:INDEL:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:44.23:FP:lm:d6_15:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:8:FP:lm:d6_15:INDEL:het	16:70936712	70902809
Common		GRCh38			16	chr16	70936712	70902809	24768	FP	ATATATATATATAT	A	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:lm:d6_15:INDEL:het	CommonFP			no		illumina reads seem to clearly support 13bp and 14bp del aligned to different locations of adjacent TR and homopolymer, and 10x is partly sepparated by haplotype and HiFi is noisy, so benchmark is likely wrong													.:.:.:.:.:NOCALL:nocall	0/1:402.73:FP:lm:d6_15:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:202.73:FP:lm:d6_15:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:lm:d6_15:INDEL:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:45.03:FP:lm:d6_15:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:8:FP:lm:d6_15:INDEL:het		70936712
Common		GRCh37			16	chr16	70961480	70927577	0	FN	CA	C,*	GT:BD:BK:BI:BVT:BLT:QQ	1|2:FN:lm:c1_5,d1_5:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no		consensus error in hifiasm from single read, coincidentally opposite a 22bp del													1|2:FN:lm:c1_5,d1_5:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:0	1|2:FN:lm:c1_5,d1_5:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:0	1|2:FN:lm:c1_5,d1_5:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:30	1|2:FN:.:c1_5,d1_5:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:0	1|2:FN:lm:c1_5,d1_5:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:0	1|2:FN:lm:c1_5,d1_5:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:0	1|2:FN:lm:c1_5,d1_5:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:0	16:70961480	70927577
Common		GRCh38			16	chr16	70961480	70927577	10642	FN	CA	C,*	GT:BD:BK:BI:BVT:BLT:QQ	1|2:FN:lm:c1_5,d1_5:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no		consensus error in hifiasm from single read, coincidentally opposite a 22bp del													1|2:FN:lm:c1_5,d1_5:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:0	1|2:FN:lm:c1_5,d1_5:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:0	1|2:FN:lm:c1_5,d1_5:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:30	1|2:FN:.:c1_5,d1_5:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:0	1|2:FN:lm:c1_5,d1_5:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:0	1|2:FN:lm:c1_5,d1_5:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:0	1|2:FN:lm:c1_5,d1_5:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:0		70961480
BCM-HGSC_xAtlas	HG002.hs37d5.60x.1_merged.vcf.gz	GRCh37	small-variants	SNP	16	chr16	70972122	70938219	18039	FP	G	T	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:18:FP:lm:tv:SNP:het 	Yes	No																															16:70972122	70938219
CMH_DRAGEN_3.6.3	NA24385.hard-filtered.vcf.gz	GRCh37	small-variants	INDEL	16	chr16	70990161	70956258	0	FP_FN	CA	C	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:42.63:d1_5:INDEL:het	yes	no	In segdup/selfchain. Not 100% sure due to conflicting reads mapped with high quality, but the fraction																														16:70990161	70956258
Common		GRCh37			16	chr16	70990161	70956258	0	FP_FN	CA	C	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:100:d1_5:INDEL:het	CommonFP_FN			no	yes	hifiasm misses ref haplotype for indel in homopolymer in highly homozygous region													1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:436.73:d1_5:INDEL:het	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:481.77:d1_5:INDEL:het	1|1:FN:am:.:d1_5:INDEL:homalt	.:.:.:30:.:NOCALL:nocall	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:319.6:d1_5:INDEL:het	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:0:d1_5:INDEL:het	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:42.63:d1_5:INDEL:het	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:16:d1_5:INDEL:het	16:70990161	70956258
Common		GRCh38			16	chr16	70990161	70956258	24276	FP_FN	CA	C	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:100:d1_5:INDEL:het	CommonFP_FN			no	yes	hifiasm misses ref haplotype for indel in homopolymer in highly homozygous region													1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:436.73:d1_5:INDEL:het	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:435.77:d1_5:INDEL:het	1|1:FN:am:.:d1_5:INDEL:homalt	.:.:.:30:.:NOCALL:nocall	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:126.6:d1_5:INDEL:het	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:0:d1_5:INDEL:het	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:42.63:d1_5:INDEL:het	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:16:d1_5:INDEL:het		70990161
BCM-HGSC_xAtlas	HG002.hs37d5.60x.1_merged.vcf.gz	GRCh37	small-variants	INDEL	16	chr16	71014437	70980534	11700	FP	T	TATATAAATATAA	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:8:FP:.:i6_15:INDEL:het 	Yes	No																															16:71014437	70980534
Common		GRCh37			16	chr16	71026137	70992234	0	FP	TA	T	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:.:d1_5:INDEL:het	CommonFP			no	yes	hifiasm misses ref haplotype for indel adjacent to short homopolymer in highly homozygous region													.:.:.:.:.:NOCALL:nocall	0/1:762.73:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:652.73:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:10:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:23.73:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:18:FP:.:d1_5:INDEL:het	16:71026137	70992234
Common		GRCh38			16	chr16	71026137	70992234	2032	FP	TA	T	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:.:d1_5:INDEL:het	CommonFP			no	yes	hifiasm misses ref haplotype for indel adjacent to short homopolymer in highly homozygous region													.:.:.:.:.:NOCALL:nocall	0/1:762.73:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:652.73:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:675.6:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:34.34:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:17:FP:.:d1_5:INDEL:het		71026137
Common		GRCh37			16	chr16	71028169	70994266	0	FP	CATGG	C	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:.:d1_5:INDEL:het	CommonFP			no	yes	hifiasm misses ref haplotype for indel in TR in highly homozygous region													.:.:.:.:.:NOCALL:nocall	0/1:1130.73:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:229.73:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:12:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:.:d1_5:INDEL:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	16:71028169	70994266
Common		GRCh38			16	chr16	71028169	70994266	25205	FP	CATGG	C	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:.:d1_5:INDEL:het	CommonFP			no	yes	hifiasm misses ref haplotype for indel in TR in highly homozygous region													.:.:.:.:.:NOCALL:nocall	0/1:1130.73:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:481.73:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:12.1:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:.:d1_5:INDEL:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.		71028169
Common		GRCh38			16	chr16	71053374	71019471	32	FP	A	G	GT:QQ:BD:BK:BI:BVT:BLT	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	CommonFP			yes		short read mapping error													./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:654.77:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:354.6:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:.:ti:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:26:FP:.:ti:SNP:het		71053374
Common		GRCh38			16	chr16	71053406	71019503	11876	FP	A	G	GT:QQ:BD:BK:BI:BVT:BLT	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	CommonFP			yes		short read mapping error													./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:636.77:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:248.6:FP:.:ti:SNP:het	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:.:ti:SNP:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:22:FP:.:ti:SNP:het		71053406
NCBI	HG002_grch38_dipcall.vcf.gz	GRCh38	small-variants	SNP	16	chr16	71065282	71031379	17231	FP_FN	C	T	GT:BD:BK:QQ:BI:BVT:BLT	1|0:FN:am:.:ti:SNP:het	1/1:FP:am:30:ti:SNP:homalt	yes	no	het correct; segdup	yes	no	short read mapping error				skip																								71065282
NCBI	HG002_grch38_dipcall.vcf.gz	GRCh38	small-variants	SNP	16	chr16	71082513	71048610	5633	FN	A	G	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	yes	no	segdup region	yes	no	segdup				skip																								71082513
Common		GRCh37			16	chr16	71088146	71054243	0	FP_FN	C	A	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:100:tv:SNP:homalt	1/1:TP:gm:100:tv:SNP:homalt	CommonFP_FN			yes	no	homozygous SNV is supported by HiFi and ONT, so low fraction of ref reads in illumina likely a result of mismapping in segdup													1|1:TP:gm:3076.77:tv:SNP:homalt	1/1:TP:gm:3076.77:tv:SNP:homalt	1|1:FN:am:.:tv:SNP:homalt	0/1:FP:am:1264.77:tv:SNP:het	1|1:TP:gm:30:tv:SNP:homalt	1/1:TP:gm:30:tv:SNP:homalt	1|1:FN:am:.:tv:SNP:homalt	0/1:FP:am:1645.6:tv:SNP:het	1|1:FN:am:.:tv:SNP:homalt	0/1:FP:am:0:tv:SNP:het	1|1:FN:am:.:tv:SNP:homalt	0/1:FP:am:49.38:tv:SNP:het	1|1:FN:am:.:tv:SNP:homalt	0/1:FP:am:23:tv:SNP:het	16:71088146	71054243
NYGC	HG-002-2x250-b38.recalibrated.haplotypeCalls.vcf.gz	GRCh38	small-variants	SNP	16	chr16	71088146	71054243	0	FP_FN	C	A	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:tv:SNP:homalt	0/1:FP:am:1283.77:tv:SNP:het 	yes	yes		yes	no	homozygous SNV is supported by HiFi and ONT, so low fraction of ref reads in illumina likely a result of mismapping in segdup																												71088146
Common		GRCh38			16	chr16	71088146	71054243	4115	FP_FN	C	A	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:100:tv:SNP:homalt	1/1:TP:gm:100:tv:SNP:homalt	CommonFP_FN			yes	no	homozygous SNV is supported by HiFi and ONT, so low fraction of ref reads in illumina likely a result of mismapping in segdup													1|1:TP:gm:3076.77:tv:SNP:homalt	1/1:TP:gm:3076.77:tv:SNP:homalt	1|1:FN:am:.:tv:SNP:homalt	0/1:FP:am:1283.77:tv:SNP:het	1|1:TP:gm:30:tv:SNP:homalt	1/1:TP:gm:30:tv:SNP:homalt	1|1:FN:am:.:tv:SNP:homalt	0/1:FP:am:1011.6:tv:SNP:het	1|1:FN:am:.:tv:SNP:homalt	0/1:FP:am:0:tv:SNP:het	1|1:FN:am:.:tv:SNP:homalt	0/1:FP:am:49.38:tv:SNP:het	1|1:FN:am:.:tv:SNP:homalt	0/1:FP:am:23:tv:SNP:het		71088146
CMH_DRAGEN_3.6.3	NA24385.hard-filtered.vcf.gz	GRCh38	small-variants	SNP	16	chr16	71092261	71058358	30806	FN	G	C	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	yes	no								skip																								71092261
NCBI	HG002_grch37_dipcall.vcf.gz	GRCh37	small-variants	SNP	16	chr16	71123067	71089164	14078	FN	T	C	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	yes	no	segdup region																														16:71123067	71089164
NYGC	HG-002-2x250-b38.recalibrated.haplotypeCalls.vcf.gz	GRCh38	small-variants	INDEL	16	chr16	71137145	71103242	28415	FN	AT	A	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:.:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0 	yes	no	The 2x250 bam has the same evidence as the pacbio and the ONT but no call in the vcf							skip																								71137145
NCBI	HG002_grch38_dipcall.vcf.gz	GRCh38	small-variants	SNP	16	chr16	71165560	71131657	10813	FN	C	T	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	yes	no	segdup region							skip																								71165560
Common		GRCh37			16	chr16	71176373	71142470	0	FN	A	AT	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:lm:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	illumina misses this ins in homopolymer due to segdup, and has good haplotype partitioning in HiFi													1|0:TP:gm:i1_5:INDEL:het:686.73	0/1:TP:gm:i1_5:INDEL:het:686.73	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:i1_5:INDEL:het:30	0/1:TP:gm:i1_5:INDEL:het:30	1|0:FN:lm:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	16:71176373	71142470
ITER	ITERteam_small-variation_GRCh38_ILMN-PB-ONT.vcf.gz	GRCh38	small-variants	INDEL	16	chr16	71176373	71142470	9943972	FP_FN	A	AT	GT:BD:BK:QQ:BI:BVT:BLT	1|0:FN:am:.:i1_5:INDEL:het	1/1:FP:am:6.9:i1_5:INDEL:homalt	Yes	No	Repetitive region of polyTs. 10x, PacBio and ONT support het genotype.	yes	no	illumina misses this ins in homopolymer due to segdup, and has good haplotype partitioning in HiFi				skip																								71176373
Roche	RN_HG002_Illumina_PacBio_Oxford_GRCh37.vcf.gz	GRCh37	small-variants	SNP	16	chr16	81120047	81086442	0	FN	A	G	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:lm:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0 	yes	no	the reason not detected by us: low-qual in our calls																														16:81120047	81086442
Roche	RN_HG002_Illumina_PacBio_Oxford.vcf.gz	GRCh38	small-variants	SNP	16	chr16	81120047	81086442	8928	FN	A	G	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:lm:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0 	yes	no	the reason not detected by us: low-qual in our calls							skip																								81120047
BCM-HGSC_xAtlas	HG002.GRCh38.60x.1_merged.vcf.gz	GRCh38	small-variants	SNP	16	chr16	81128975	81095370	7342434	FP_FN	C	T	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:ti:SNP:homalt	0/1:FP:am:28:ti:SNP:het 	Yes	No								skip																								81128975
NCBI	HG002_grch38_dipcall.vcf.gz	GRCh38	small-variants	SNP	16	chr16	88504212	88437804	743170	FP	G	C	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:lm:tv:SNP:het	yes	no	ONT data show DELs nearby	R in query						skip																								88504212
Common		GRCh37			16	chr16	89247382	89180974	0	FP_FN	C	CTTTTTTTTTTTTTTTTTTT,CTTTTTTTTTTTTTTT,CTTTTTTTTTTTTTTTT,CTTTTTTTTTTTTTTTTTT	GT:BD:BK:BI:BVT:BLT:QQ	1|2:FN:am:i16_plus,i6_15:INDEL:hetalt:.	2/2:FP:am:i6_15:INDEL:homalt:100	CommonFP_FN			unsure		benchmark appears correct based on average of HiFi haplotypes but few illumina reads cross homopolymer and insertions make very long homopolymer													1|2:FN:lm:i16_plus,i6_15:INDEL:hetalt:.	4/4:FP:lm:i16_plus:INDEL:homalt:1060.73	1|2:FN:.:i16_plus,i6_15:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:0	1|2:FN:lm:i16_plus,i6_15:INDEL:hetalt:.	3/3:FP:lm:i16_plus:INDEL:homalt:30	1|2:FN:lm:i16_plus,i6_15:INDEL:hetalt:.	3/3:FP:lm:i16_plus:INDEL:homalt:76.98	1|2:FN:.:i16_plus,i6_15:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:0	1|2:FN:am:i16_plus,i6_15:INDEL:hetalt:.	2/2:FP:am:i6_15:INDEL:homalt:72.62	1|2:FN:.:i16_plus,i6_15:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:0	16:89247382	89180974
Common		GRCh38			16	chr16	89247382	89180974	193363	FP_FN	C	CTTTTTTTTTTTTTTT,CTTTTTTTTTTTTTTTTTTT,CTTTTTTTTTTTTTTTTTT,CTTTTTTTTTTTTTTTT	GT:BD:BK:BI:QQ:BVT:BLT	2|1:FN:am:i16_plus,i6_15:.:INDEL:hetalt	1/1:FP:am:i6_15:100:INDEL:homalt	CommonFP_FN			unsure		benchmark appears correct based on average of HiFi haplotypes but few illumina reads cross homopolymer and insertions make very long homopolymer													2|1:FN:lm:i16_plus,i6_15:.:INDEL:hetalt	3/3:FP:lm:i16_plus:1060.73:INDEL:homalt	2|1:FN:am:i16_plus,i6_15:.:INDEL:hetalt	1/1:FP:am:i6_15:252.77:INDEL:homalt	2|1:FN:lm:i16_plus,i6_15:.:INDEL:hetalt	4/4:FP:lm:i16_plus:30:INDEL:homalt	2|1:FN:am:i16_plus,i6_15:.:INDEL:hetalt	0/1:FP:am:i6_15:198.64:INDEL:het	2|1:FN:.:i16_plus,i6_15:.:INDEL:hetalt	.:.:.:.:0:NOCALL:nocall	2|1:FN:am:i16_plus,i6_15:.:INDEL:hetalt	1/1:FP:am:i6_15:72.59:INDEL:homalt	2|1:FN:.:i16_plus,i6_15:.:INDEL:hetalt	.:.:.:.:0:NOCALL:nocall		89247382
Common		GRCh37			16	chr16	89440745	89374337	48034	FP_FN	T	TA	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:100:i1_5:INDEL:het	CommonFP_FN			no	yes	hifiasm misses ref haplotype for this ins in long homopolymer due to homozygous region													1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:271.73:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:443.73:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:30:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:469.64:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:0:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:50:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:9:i1_5:INDEL:het	16:89440745	89374337
PacBio_gatk4	gatk4hc_HG002_15kb_20kb_53X_SequelII.vcf.gz	GRCh38	small-variants	SNP	16	chr16	89488779	89422371	-88400251	FP_FN	A	T	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:tv:SNP:homalt	0/1:FP:am:2022.77:tv:SNP:het	yes	no								skip																								89488779
BCM-HGSC_xAtlas	HG002.GRCh38.60x.1_merged.vcf.gz	GRCh38	small-variants	INDEL	17	chr17	925360	1022120	2663	FN	A	AAAAAAAAAAAC	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:.:i6_15:INDEL:het:.	.:.:.:.:NOCALL:nocall:0 	Yes	No								skip																								925360
Common		GRCh37			17	chr17	928023	1024783	0	FP_FN	CAAA	C,CAAAA	GT:BD:BK:BI:QQ:BVT:BLT	2|1:FN:am:d1_5,i1_5:.:INDEL:hetalt	0/1:FP:am:d1_5:100:INDEL:het	CommonFP_FN			no	yes	benchmark has ins on one haplotype likely due to noise in HiFi though even illumina is noisy													2|1:FN:am:d1_5,i1_5:.:INDEL:hetalt	0/1:FP:am:d1_5:419.14:INDEL:het	2|1:FN:am:d1_5,i1_5:.:INDEL:hetalt	0/1:FP:am:d1_5:300.77:INDEL:het	2|1:FN:am:d1_5,i1_5:.:INDEL:hetalt	0/1:FP:am:d1_5:30:INDEL:het	2|1:FN:am:d1_5,i1_5:.:INDEL:hetalt	0/1:FP:am:d1_5:201.6:INDEL:het	2|1:FN:am:d1_5,i1_5:.:INDEL:hetalt	0/1:FP:am:d1_5:0:INDEL:het	2|1:FN:am:d1_5,i1_5:.:INDEL:hetalt	0/1:FP:am:d1_5:50:INDEL:het	2|1:FN:am:d1_5,i1_5:.:INDEL:hetalt	0/1:FP:am:d1_5:6:INDEL:het	17:928023	1024783
Common		GRCh38			17	chr17	928023	1024783	3433	FP_FN	CAAA	C,CAAAA	GT:BD:BK:BI:QQ:BVT:BLT	2|1:FN:am:d1_5,i1_5:.:INDEL:hetalt	0/1:FP:am:d1_5:100:INDEL:het	CommonFP_FN			no	yes	benchmark has ins on one haplotype likely due to noise in HiFi though even illumina is noisy													2|1:FN:am:d1_5,i1_5:.:INDEL:hetalt	0/1:FP:am:d1_5:419.14:INDEL:het	2|1:FN:am:d1_5,i1_5:.:INDEL:hetalt	0/1:FP:am:d1_5:295.77:INDEL:het	2|1:FN:am:d1_5,i1_5:.:INDEL:hetalt	0/1:FP:am:d1_5:30:INDEL:het	2|1:FN:.:d1_5,i1_5:.:INDEL:hetalt	.:.:.:.:0:NOCALL:nocall	2|1:FN:am:d1_5,i1_5:.:INDEL:hetalt	0/1:FP:am:d1_5:0:INDEL:het	2|1:FN:am:d1_5,i1_5:.:INDEL:hetalt	0/1:FP:am:d1_5:50:INDEL:het	2|1:FN:am:d1_5,i1_5:.:INDEL:hetalt	0/1:FP:am:d1_5:6:INDEL:het		928023
Roche	RN_HG002_Illumina_PacBio_Oxford.vcf.gz	GRCh38	small-variants	SNP	17	chr17	931456	1028216	886	FN	T	G	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:lm:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0 	yes	no	the reason not detected by us: low-qual in our calls							skip																								931456
ITER	ITERteam_small-variation_GRCh38_ILMN-PB-ONT.vcf.gz	GRCh38	small-variants	INDEL	17	chr17	932342	1029102	3283	FN	CA	C	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:.:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	Yes	No	Detected by ILMN, 10x and ONT in truth. No detected by query because of MQ=0.							skip																								932342
Common		GRCh37			17	chr17	935625	1032385	0	FN	TC	T	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no		Series of variants in the benchmark that appear to all come from the same read, likely resulting from the consensus issue in hifiasmv0.11 that was mostly corrected in v0.13													1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	17:935625	1032385
Common		GRCh38			17	chr17	935625	1032385	261	FN	TC	T	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no		Series of variants in the benchmark that appear to all come from the same read, likely resulting from the consensus issue in hifiasmv0.11 that was mostly corrected in v0.13													.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0			935625
DNAnexus	GRCh38_HG002_WGS_union.vcf.gz	GRCh38	small-variants	SNP	17	chr17	935886	1032646	252	FP	T	C	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:lm:ti:SNP:het 	yes	no	Illumina -  ~15% C calls 10x - ~15% C calls Others- 100%T calls 	yes	no	Short read error due to missing 41bp ins				skip																								935886
Common		GRCh37			17	chr17	936138	1032898	0	FN	TG	T	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no		Series of variants in the benchmark that appear to all come from the same read, likely resulting from the consensus issue in hifiasmv0.11 that was mostly corrected in v0.15													1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	17:936138	1032898
Common		GRCh38			17	chr17	936138	1032898	98	FN	TG	T	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no		Series of variants in the benchmark that appear to all come from the same read, likely resulting from the consensus issue in hifiasmv0.11 that was mostly corrected in v0.15													.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0			936138
Common		GRCh37			17	chr17	936236	1032996	0	FN	AG	A	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no		Series of variants in the benchmark that appear to all come from the same read, likely resulting from the consensus issue in hifiasmv0.11 that was mostly corrected in v0.16													1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	17:936236	1032996
Common		GRCh38			17	chr17	936236	1032996	108	FN	AG	A	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no		Series of variants in the benchmark that appear to all come from the same read, likely resulting from the consensus issue in hifiasmv0.11 that was mostly corrected in v0.16													.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0			936236
Common		GRCh37			17	chr17	936344	1033104	0	FN	T	TG	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no		Series of variants in the benchmark that appear to all come from the same read, likely resulting from the consensus issue in hifiasmv0.11 that was mostly corrected in v0.17													1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	17:936344	1033104
Common		GRCh38			17	chr17	936344	1033104	380	FN	T	TG	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no		Series of variants in the benchmark that appear to all come from the same read, likely resulting from the consensus issue in hifiasmv0.11 that was mostly corrected in v0.17													.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0			936344
Common		GRCh37			17	chr17	936724	1033484	0	FN	TC	T	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no		Series of variants in the benchmark that appear to all come from the same read, likely resulting from the consensus issue in hifiasmv0.11 that was mostly corrected in v0.18													1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	17:936724	1033484
Common		GRCh38			17	chr17	936724	1033484	186	FN	TC	T	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no		Series of variants in the benchmark that appear to all come from the same read, likely resulting from the consensus issue in hifiasmv0.11 that was mostly corrected in v0.18													.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0			936724
Common		GRCh37			17	chr17	936910	1033670	0	FN	T	TCA	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no		Series of variants in the benchmark that appear to all come from the same read, likely resulting from the consensus issue in hifiasmv0.11 that was mostly corrected in v0.18													1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	17:936910	1033670
Common		GRCh38			17	chr17	936910	1033670	41	FN	T	TCA	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no		Series of variants in the benchmark that appear to all come from the same read, likely resulting from the consensus issue in hifiasmv0.11 that was mostly corrected in v0.19													.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0			936910
Common		GRCh37			17	chr17	936951	1033711	0	FN	C	A	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no		Series of variants in the benchmark that appear to all come from the same read, likely resulting from the consensus issue in hifiasmv0.11 that was mostly corrected in v0.18													1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	17:936951	1033711
Common		GRCh38			17	chr17	936951	1033711	1194	FN	C	A	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no		Series of variants in the benchmark that appear to all come from the same read, likely resulting from the consensus issue in hifiasmv0.11 that was mostly corrected in v0.20													.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0			936951
Common		GRCh37			17	chr17	938145	1034905	0	FN	CG	C	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no		Series of variants in the benchmark that appear to all come from the same read, likely resulting from the consensus issue in hifiasmv0.11 that was mostly corrected in v0.18													1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	17:938145	1034905
Common		GRCh38			17	chr17	938145	1034905	175	FN	CG	C	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no		Series of variants in the benchmark that appear to all come from the same read, likely resulting from the consensus issue in hifiasmv0.11 that was mostly corrected in v0.21													.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0			938145
Common		GRCh37			17	chr17	938320	1035080	0	FN	T	TG	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no		Series of variants in the benchmark that appear to all come from the same read, likely resulting from the consensus issue in hifiasmv0.11 that was mostly corrected in v0.18													1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	17:938320	1035080
Common		GRCh38			17	chr17	938320	1035080	130	FN	T	TG	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no		Series of variants in the benchmark that appear to all come from the same read, likely resulting from the consensus issue in hifiasmv0.11 that was mostly corrected in v0.22													.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0			938320
Common		GRCh37			17	chr17	938450	1035210	0	FN	T	TC	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no		Series of variants in the benchmark that appear to all come from the same read, likely resulting from the consensus issue in hifiasmv0.11 that was mostly corrected in v0.18													1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	17:938450	1035210
ITER	ITERteam_small-variation_GRCh38_ILMN-PB-ONT.vcf.gz	GRCh38	small-variants	INDEL	17	chr17	938450	1035210	0	FN	T	TC	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	No	Yes	No support in both truth and query. No technology called the variant.	no	yes	Series of variants in the benchmark that appear to all come from the same read, likely resulting from the consensus issue in hifiasmv0.11 that was mostly corrected in v0.23				no	see note	There does not appear to be any support for insertion with the exception of one read in HiFi and a few in ONT.  nearby variant (1035246) in query does not appear to be correct.  They call a HOM_VAR however I don't see evidence for variant called (insertion)																						938450
Common		GRCh38			17	chr17	938450	1035210	59310	FN	T	TC	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no		Series of variants in the benchmark that appear to all come from the same read, likely resulting from the consensus issue in hifiasmv0.11 that was mostly corrected in v0.24													.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0			938450
ITER	ITERteam_small-variation_GRCh38_ILMN-PB-ONT.vcf.gz	GRCh38	small-variants	SNP	17	chr17	997760	1094520	1166	FN	A	G	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	Yes	No	All technologies in truth called this variant. Low MQ in query.																															997760
DNAnexus	hs37d5_HG002_WGS_union.vcf.gz	GRCh37	small-variants	SNP	17	chr17	998926	1095686	4654	FN	A	G	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	yes	no																															17:998926	1095686
ITER	ITERteam_small-variation_GRCh38_ILMN-PB-ONT.vcf.gz	GRCh38	small-variants	SNP	17	chr17	1003580	1100340	59942	FP_FN	A	G	GT:BD:BK:QQ:BI:BVT:BLT	1|0:FN:am:.:ti:SNP:het	1/1:FP:am:11.1:ti:SNP:homalt	Yes	No	Het genotype well supported by all technologies in truth. Query reads have low MQ and fewer reads in comparison to truth.							skip																								1003580
Common		GRCh37			17	chr17	1063576	1160282	0	FP	CCA	C	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:lm:d1_5:INDEL:het	CommonFP			no	yes	benchmark should have extra homopolymer base deleted in adjacent homopolymer and diTR													.:.:.:.:.:NOCALL:nocall	0/1:125.73:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:861.73:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:570.6:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:48.91:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:9:FP:lm:d1_5:INDEL:het	17:1063576	1160282
Common		GRCh37			17	chr17	1063576	1160282	1	FN	C	A	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:lm:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no	yes	benchmark should have extra homopolymer base deleted in adjacent homopolymer and diTR													1|0:FN:lm:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:lm:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:lm:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:lm:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:lm:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:lm:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:lm:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	17:1063576	1160282
Common		GRCh37			17	chr17	1063577	1160283	18281	FN	CA	C	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:lm:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no	yes	benchmark should have extra homopolymer base deleted in adjacent homopolymer and diTR													1|0:FN:lm:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:lm:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:lm:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:lm:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:lm:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:lm:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:lm:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	17:1063577	1160283
NCBI	HG002_grch37_dipcall.vcf.gz	GRCh37	small-variants	INDEL	17	chr17	1081858	1178564	440	FP	C	CA	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:lm:i1_5:INDEL:het	unsure	unsure	repeat region; multiple As here; some evidence for HET INS; AG INS at pos 1081870	yes	no	benchmark call supported by illumina reads that traverse homopolymer region																											17:1081858	1178564
ITER	ITERteam_small-variation_GRCh37_ILMN-PB-ONT.vcf.gz	GRCh37	small-variants	INDEL	17	chr17	1082298	1179004	16293	FP	GT	G	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:7.1:FP:.:d1_5:INDEL:het	Yes	No																															17:1082298	1179004
Common		GRCh37			17	chr17	1098591	1195297	0	FN	ACTGT	A	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:lm:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no		hifiasm misses shorter ins on one haplotype likely due to homozygous region and homopolymer													1|1:FN:lm:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:lm:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:d1_5:INDEL:homalt:30	1/1:TP:gm:d1_5:INDEL:homalt:30	1|1:FN:lm:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:lm:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:d1_5:INDEL:homalt:66.26	.:.:.:.:NOCALL:nocall:0	1|1:FN:lm:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	17:1098591	1195297
Common		GRCh38			17	chr17	1098591	1195297	7	FN	ACTGT	A	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:lm:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no		hifiasm misses shorter ins on one haplotype likely due to homozygous region and homopolymer													1|1:FN:lm:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:lm:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:d1_5:INDEL:homalt:30	1/1:TP:gm:d1_5:INDEL:homalt:30	1|1:TP:gm:d1_5:INDEL:homalt:481.02	.:.:.:.:NOCALL:nocall:0	1|1:FN:lm:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:d1_5:INDEL:homalt:66.26	.:.:.:.:NOCALL:nocall:0	1|1:FN:lm:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0		1098591
ITER	ITERteam_small-variation_GRCh37_ILMN-PB-ONT.vcf.gz	GRCh37	small-variants	INDEL	17	chr17	1098598	1195304	1109076	FP_FN	C	CA,CAA,CCGTTGCAAAAAAAAAA	GT:BD:BK:QQ:BI:BVT:BLT	3|3:FN:lm:.:i16_plus:INDEL:homalt	2/1:FP:lm:12.8:i1_5:INDEL:hetalt	Yes	No		no		hifiasm misses shorter ins on one haplotype likely due to homozygous region and homopolymer																											17:1098598	1195304
ITER	ITERteam_small-variation_GRCh37_ILMN-PB-ONT.vcf.gz	GRCh37	small-variants	SNP	17	chr17	2207674	2304380	1388747	FP	T	A	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:813.6:FP:lm:tv:SNP:het	Yes	No																															17:2207674	2304380
PacBio_gatk4	gatk4hc_HG002_15kb_20kb_53X_SequelII.vcf.gz	GRCh38	small-variants	INDEL	17	chr17	3596421	3693127	14326020	FN	C	CA,CAA	GT:BD:BK:BI:BVT:BLT:QQ	1|2:FN:.:i1_5:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:0	yes	no								skip																								3596421
Common		GRCh37			17	chr17	17922461	18019147	0	FP	C	CCA,CCACACA	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	2/1:100:FP:.:i1_5,i6_15:INDEL:hetalt	CommonFP			no	yes	hifiasm error in diTR due to highly homozygous region and noisy TR													.:.:.:.:.:NOCALL:nocall	2/1:873.73:FP:.:i1_5,i6_15:INDEL:hetalt	.:.:.:.:.:NOCALL:nocall	2/1:1022.73:FP:.:i1_5,i6_15:INDEL:hetalt	.:.:.:.:.:NOCALL:nocall	1/1:30:FP:.:i1_5:INDEL:homalt	.:.:.:.:.:NOCALL:nocall	2/1:480.1:FP:.:i1_5,i6_15:INDEL:hetalt	.:.:.:.:.:NOCALL:nocall	2/1:0:FP:.:i1_5,i6_15:INDEL:hetalt	.:.:.:.:.:NOCALL:nocall	2/1:186.35:FP:.:i1_5,i6_15:INDEL:hetalt	.:.:.:.:.:NOCALL:nocall	0/1:7:FP:.:i1_5:INDEL:het	17:17922461	18019147
Common		GRCh38			17	chr17	17922461	18019147	39	FP	C	CCA,CCACACA	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	2/1:100:FP:.:i1_5,i6_15:INDEL:hetalt	CommonFP			no	yes	hifiasm error in diTR due to highly homozygous region and noisy TR													.:.:.:.:.:NOCALL:nocall	2/1:873.73:FP:.:i1_5,i6_15:INDEL:hetalt	.:.:.:.:.:NOCALL:nocall	2/1:1055.73:FP:.:i1_5,i6_15:INDEL:hetalt	.:.:.:.:.:NOCALL:nocall	1/1:30:FP:.:i1_5:INDEL:homalt	.:.:.:.:.:NOCALL:nocall	2/1:1038.1:FP:.:i1_5,i6_15:INDEL:hetalt	.:.:.:.:.:NOCALL:nocall	2/1:0:FP:.:i1_5,i6_15:INDEL:hetalt	.:.:.:.:.:NOCALL:nocall	2/1:186.22:FP:.:i1_5,i6_15:INDEL:hetalt	.:.:.:.:.:NOCALL:nocall	0/1:7:FP:.:i1_5:INDEL:het		17922461
Common		GRCh37			17	chr17	17922500	18019186	0	FN	C	CACACA	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no	yes	hifiasm error in diTR due to highly homozygous region and noisy TR													1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	17:17922500	18019186
Common		GRCh38			17	chr17	17922500	18019186	13976669	FN	C	CACACA	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no	yes	hifiasm error in diTR due to highly homozygous region and noisy TR													1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0		17922500
Common		GRCh37			17	chr17	30322874	31995855	0	FP	C	CT	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:22.0103:FP:.:i1_5:INDEL:het	CommonFP			no	yes	these 2 nearby errors in benchmark might result from hifiasm consensus error													.:.:.:.:.:NOCALL:nocall	0/1:123.73:FP:.:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:403.73:FP:.:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:.:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:686.64:FP:.:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:.:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:43.37:FP:.:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:17:FP:.:i1_5:INDEL:het	17:30322874	31995855
CMH_DRAGEN_3.6.3	NA24385.hard-filtered.vcf.gz	GRCh38	small-variants	INDEL	17	chr17	30322874	31995855	0	FP	C	CT	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:43.38:FP:.:i1_5:INDEL:het	no	yes	The query is well supported by PacBio/ILMN and reads are aligned with high MQ	no	yes	these 2 nearby errors in benchmark might result from hifiasm consensus error				no	yes	appears to be support for HET in all technologies and within HP in thrid gen.																						30322874
Common		GRCh38			17	chr17	30322874	31995855	131	FP	C	CT	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:20.9193:FP:.:i1_5:INDEL:het	CommonFP			no	yes	these 2 nearby errors in benchmark might result from hifiasm consensus error													.:.:.:.:.:NOCALL:nocall	0/1:123.73:FP:.:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:403.73:FP:.:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:.:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:204.64:FP:.:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:.:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:43.38:FP:.:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:17:FP:.:i1_5:INDEL:het		30322874
NCBI	HG002_grch37_dipcall.vcf.gz	GRCh37	small-variants	INDEL	17	chr17	30323005	31995986	0	FN	A	AT	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	no	yes	no evidence for benchmark; repeat region	no	yes	these 2 nearby errors in benchmark might result from hifiasm consensus error																											17:30323005	31995986
Common		GRCh37			17	chr17	30323005	31995986	0	FN	A	AT	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no	yes	these 2 nearby errors in benchmark might result from hifiasm consensus error													1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	17:30323005	31995986
Common		GRCh38			17	chr17	30323005	31995986	16969152	FN	A	AT	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no	yes	these 2 nearby errors in benchmark might result from hifiasm consensus error													1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0		30323005
DNAnexus	hs37d5_HG002_WGS_union.vcf.gz	GRCh37	small-variants	INDEL	17	chr17	47042500	48965138	2821	FP	C	CA,CAA	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	2/1:0:FP:lm:i1_5:INDEL:hetalt	unsure	yes	This is a homopolymer seuqence. The reference genome has 13 consecutive A's. Both the benchmark and the query callset called this deletion. This should not be a FP. Instead, this is just a difference in how to genotype format is presented.	yes	no	benchmark call supported by illumina reads that traverse homopolymer region. Query doesn't call all variants in both haplotypes in the region																											17:47042500	48965138
DNAnexus	GRCh38_HG002_WGS_union.vcf.gz	GRCh38	small-variants	SNP	17	chr17	47045321	48967959	29160839	FN	T	C	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0 	yes	no								skip																								47045321
Common		GRCh37			17	chr17	76124879	78128798	2178564	FP_FN	CGG	C,CGGGG	GT:BD:BK:BI:QQ:BVT:BLT	2|1:TP:gm:d1_5,i1_5:100:INDEL:hetalt	0/1:TP:gm:d1_5:100:INDEL:het	CommonFP_FN			no	yes	benchmark is almost correct in G homopolymer, but calls wrong ins length													2|1:TP:gm:d1_5,i1_5:1077.73:INDEL:hetalt	0/1:TP:gm:d1_5:1077.73:INDEL:het	2|1:FN:am:d1_5,i1_5:.:INDEL:hetalt	0/1:FP:am:d1_5:535.73:INDEL:het	2|1:FN:am:d1_5,i1_5:.:INDEL:hetalt	1/1:FP:am:d1_5:30:INDEL:homalt	2|1:FN:am:d1_5,i1_5:.:INDEL:hetalt	0/1:FP:am:d1_5:778.6:INDEL:het	2|1:FN:am:d1_5,i1_5:.:INDEL:hetalt	0/1:FP:am:d1_5:0:INDEL:het	2|1:FN:am:d1_5,i1_5:.:INDEL:hetalt	0/1:FP:am:d1_5:161.21:INDEL:het	2|1:FN:am:d1_5,i1_5:.:INDEL:hetalt	0/1:FP:am:d1_5:15:INDEL:het	17:76124879	78128798
Common		GRCh37			17	chr17	78281162	80307362	80261	FP_FN	G	GT,GTT	GT:BD:BK:QQ:BI:BVT:BLT	2|0:FN:lm:.:i1_5:INDEL:het	0/1:FP:lm:100:i1_5:INDEL:het	CommonFP_FN			no	yes	benchmark has wrong ins length in long homopolymer													2|0:FN:.:.:i1_5:INDEL:het	.:.:.:0:.:NOCALL:nocall	2|0:FN:lm:.:i1_5:INDEL:het	0/1:FP:lm:130.73:i1_5:INDEL:het	2|0:FN:lm:.:i1_5:INDEL:het	1/1:FP:lm:30:i1_5:INDEL:homalt	2|0:FN:lm:.:i1_5:INDEL:het	0/1:FP:lm:146.64:i1_5:INDEL:het	2|0:FN:.:.:i1_5:INDEL:het	.:.:.:0:.:NOCALL:nocall	2|0:FN:lm:.:i1_5:INDEL:het	0/1:FP:lm:48.66:i1_5:INDEL:het	2|0:FN:lm:.:i1_5:INDEL:het	0/1:FP:lm:9:i1_5:INDEL:het	17:78281162	80307362
NCBI	HG002_grch38_dipcall.vcf.gz	GRCh38	small-variants	INDEL	17	chr17	78361423	80387623	6246	FP	C	CCG	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:lm:i1_5:INDEL:het	yes	no	chr17:80387624 SNP for both							skip																								78361423
Common		GRCh37			17	chr17	78367669	80393869	0	FN	CT	C	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no	yes	hifiasm error due to HiFi noise in ~10bp homopolymer													0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	17:78367669	80393869
Common		GRCh38			17	chr17	78367669	80393869	2863	FN	CT	C	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no	yes	hifiasm error due to HiFi noise in ~10bp homopolymer													0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0		78367669
BCM-HGSC_xAtlas	HG002.hs37d5.60x.1_merged.vcf.gz	GRCh37	small-variants	INDEL	17	chr17	78370532	80396732	12	FP	CCA	C	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:6:FP:lm:d1_5:INDEL:het 	Yes	No																															17:78370532	80396732
Common		GRCh37			17	chr17	78370544	80396744	-79732978	FN	C	CA	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:lm:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			unsure	unsure	all techs noisy in long C homopolymer													1|0:TP:gm:i1_5:INDEL:het:634.73	0/1:TP:gm:i1_5:INDEL:het:634.73	1|0:FN:lm:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:lm:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	1|0:TP:gm:i1_5:INDEL:het:0	0/1:TP:gm:i1_5:INDEL:het:0	1|0:FN:lm:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:lm:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	17:78370544	80396744
CMH_DRAGEN_3.6.3	NA24385.hard-filtered.vcf.gz	GRCh37	small-variants	SNP	18	chr18	663766	663766	4226	FN	A	C	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	yes	no																															18:663766	663766
Common		GRCh37			18	chr18	667992	667992	0	FP_FN	A	ATTTTTTTTTTTTT,ATTTTTTTTTTTTTT	GT:BD:BK:BI:BVT:BLT:QQ	2|1:FN:am:i6_15:INDEL:hetalt:.	0/1:FP:am:i6_15:INDEL:het:100	CommonFP_FN			no	unsure	insertion causes >20bp A homopolymer on both haplotypes which causes noisy HiFi reads and only a few illumina reads crossing the homopolymer													2|1:FN:.:i6_15:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:0	2|1:FN:.:i6_15:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:0	2|1:FN:am:i6_15:INDEL:hetalt:.	1/1:FP:am:i6_15:INDEL:homalt:30	2|1:FN:am:i6_15:INDEL:hetalt:.	1/1:FP:am:i6_15:INDEL:homalt:253.96	2|1:FN:am:i6_15:INDEL:hetalt:.	1/1:FP:am:i6_15:INDEL:homalt:0	2|1:FN:am:i6_15:INDEL:hetalt:.	1/1:FP:am:i6_15:INDEL:homalt:91.39	2|1:FN:.:i6_15:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:0	18:667992	667992
NCBI	HG002_grch38_dipcall.vcf.gz	GRCh38	small-variants	INDEL	18	chr18	667992	667992	0	FP_FN	A	ATTTTTTTTTTTTT,ATTTTTTTTTTTTTT	GT:BD:BK:BI:QQ:BVT:BLT	2|1:FN:am:i6_15:.:INDEL:hetalt	1/1:FP:am:i6_15:30:INDEL:homalt	no	yes	evidences for HOM rather HET here	no	unsure	insertion causes >20bp A homopolymer on both haplotypes which causes noisy HiFi reads and only a few illumina reads crossing the homopolymer				unsure	yes	homopolymer. coverage is low for 10X and ILMN have few reads that span hompolymer, however of the ones that do they support an insertion.Hifi supports variety of insertion length as does ONT.  It would be difficult to pin down an insertion length. 																						667992
CMH_DRAGEN_3.6.3	NA24385.hard-filtered.vcf.gz	GRCh38	small-variants	INDEL	18	chr18	667992	667992	76603254	FP_FN	A	ATTTTTTTTTTTTT,ATTTTTTTTTTTTTT	GT:BD:BK:BI:QQ:BVT:BLT	2|1:FN:am:i6_15:.:INDEL:hetalt	1/1:FP:am:i6_15:91.39:INDEL:homalt	unsure	unsure	Conflicting evidences exist. Can't tell reliably that two polyA alleles differ by one in length.	no	unsure	insertion causes >20bp A homopolymer on both haplotypes which causes noisy HiFi reads and only a few illumina reads crossing the homopolymer																												667992
Common		GRCh38			18	chr18	74983202	77271246	2472280	FP_FN	A	AC	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:36.9896:i1_5:INDEL:het	CommonFP_FN			unsure	unsure	all techs noisy in C homopolymer													1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:415.73:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:126.78:i1_5:INDEL:het	1|1:TP:gm:30:i1_5:INDEL:homalt	1/1:TP:gm:30:i1_5:INDEL:homalt	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:73.64:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:0:i1_5:INDEL:het	1|1:FN:.:.:i1_5:INDEL:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:i1_5:INDEL:homalt	.:.:.:0:.:NOCALL:nocall		74983202
Common		GRCh37			18	chr18	77503526	79743526	-78558009	FP_FN	C	CA,CAA	GT:BD:BK:BI:QQ:BVT:BLT	2|1:TP:gm:i1_5:100:INDEL:hetalt	2/1:TP:gm:i1_5:100:INDEL:hetalt	CommonFP_FN			yes	no	benchmark supported by illumina in long homopolymer													2|1:FN:am:i1_5:.:INDEL:hetalt	1/1:FP:am:i1_5:442.73:INDEL:homalt	2|1:FN:am:i1_5:.:INDEL:hetalt	1/1:FP:am:i1_5:386.73:INDEL:homalt	2|1:FN:am:i1_5:.:INDEL:hetalt	2/2:FP:am:i1_5:30:INDEL:homalt	2|1:FN:am:i1_5:.:INDEL:hetalt	0/2:FP:am:i1_5:71.64:INDEL:het	2|1:TP:gm:i1_5:0:INDEL:hetalt	1/1:FP:lm:i1_5:0:INDEL:homalt	2|1:TP:gm:i1_5:168.21:INDEL:hetalt	2/1:TP:gm:i1_5:168.21:INDEL:hetalt	2|1:FN:am:i1_5:.:INDEL:hetalt	1/1:FP:am:i1_5:15:INDEL:homalt	18:77503526	79743526
Common		GRCh38			19	chr19	1185516	1185517	5213	FP_FN	C	CA	GT:BD:BK:QQ:BI:BVT:BLT	1|0:FN:am:.:i1_5:INDEL:het	1/1:FP:am:100:i1_5:INDEL:homalt	CommonFP_FN			no	yes	illumina is almost all 1bp ins so likely an error due to noise in HiFi data on each haplotype													1|0:FN:am:.:i1_5:INDEL:het	1/1:FP:am:240.73:i1_5:INDEL:homalt	1|0:FN:am:.:i1_5:INDEL:het	1/1:FP:am:538.73:i1_5:INDEL:homalt	1|0:FN:am:.:i1_5:INDEL:het	1/1:FP:am:30:i1_5:INDEL:homalt	.:.:.:.:.:NOCALL:nocall	0/1:TP:gm:320.13:i1_5:INDEL:het	1|0:FN:am:.:i1_5:INDEL:het	1/1:FP:am:0:i1_5:INDEL:homalt	1|0:FN:am:.:i1_5:INDEL:het	1/1:FP:am:124.91:i1_5:INDEL:homalt	1|0:FN:am:.:i1_5:INDEL:het	1/1:FP:am:11:i1_5:INDEL:homalt		1185516
Common		GRCh37			19	chr19	1190729	1190730	0	FP_FN	C	CA,CAA	GT:BD:BK:BI:QQ:BVT:BLT	1|2:FN:am:i1_5:.:INDEL:hetalt	1/1:FP:am:i1_5:100:INDEL:homalt	CommonFP_FN			no	yes	illumina is almost all 1bp ins so likely an error due to noise in HiFi data on each haplotype													1|2:FN:am:i1_5:.:INDEL:hetalt	1/1:FP:am:i1_5:128:INDEL:homalt	1|2:FN:am:i1_5:.:INDEL:hetalt	1/1:FP:am:i1_5:792.73:INDEL:homalt	1|2:FN:am:i1_5:.:INDEL:hetalt	1/1:FP:am:i1_5:30:INDEL:homalt	1|2:FN:am:i1_5:.:INDEL:hetalt	1/1:FP:am:i1_5:249.06:INDEL:homalt	1|2:FN:am:i1_5:.:INDEL:hetalt	1/1:FP:am:i1_5:0:INDEL:homalt	1|2:FN:am:i1_5:.:INDEL:hetalt	1/1:FP:am:i1_5:119.78:INDEL:homalt	1|2:FN:am:i1_5:.:INDEL:hetalt	1/1:FP:am:i1_5:10:INDEL:homalt	19:1190729	1190730
ITER	ITERteam_small-variation_GRCh38_ILMN-PB-ONT.vcf.gz	GRCh38	small-variants	INDEL	19	chr19	1190729	1190730	0	FP_FN	C	CA,CAA	GT:BD:BK:BI:QQ:BVT:BLT	1|2:FN:am:i1_5:.:INDEL:hetalt	1/1:FP:am:i1_5:431.06:INDEL:homalt	Unsure	Unsure	1nt insertion genotype in query is well supported by ILMN, and 2nt insertion is supported by PacBio in truth. Repetitive region of polyAs.	no	yes	illumina is almost all 1bp ins so likely an error due to noise in HiFi data on each haplotype				no	yes	homopolymer in SINE. ILMN, 10X, Hifi have support for complex HET (REF and both ALTS) however predominate support is for single bp insertion (particularly ILMN). Hifi has a bit more suport for 2bp insert and insert sizes vary across HP. 																						1190729
Common		GRCh38			19	chr19	1190729	1190730	2720	FP_FN	C	CA,CAA	GT:BD:BK:BI:QQ:BVT:BLT	1|2:FN:am:i1_5:.:INDEL:hetalt	1/1:FP:am:i1_5:100:INDEL:homalt	CommonFP_FN			no	yes	illumina is almost all 1bp ins so likely an error due to noise in HiFi data on each haplotype													1|2:FN:am:i1_5:.:INDEL:hetalt	1/1:FP:am:i1_5:128:INDEL:homalt	1|2:FN:am:i1_5:.:INDEL:hetalt	1/1:FP:am:i1_5:831.77:INDEL:homalt	1|2:FN:am:i1_5:.:INDEL:hetalt	1/1:FP:am:i1_5:30:INDEL:homalt	1|2:FN:am:i1_5:.:INDEL:hetalt	1/1:FP:am:i1_5:431.06:INDEL:homalt	1|2:FN:am:i1_5:.:INDEL:hetalt	1/1:FP:am:i1_5:0:INDEL:homalt	1|2:FN:am:i1_5:.:INDEL:hetalt	1/1:FP:am:i1_5:119.77:INDEL:homalt	1|2:FN:am:i1_5:.:INDEL:hetalt	1/1:FP:am:i1_5:10:INDEL:homalt		1190729
Roche	RN_HG002_Illumina_PacBio_Oxford_GRCh37.vcf.gz	GRCh37	small-variants	INDEL	19	chr19	1193449	1193450	0	FP_FN	CA	C,CAAA	GT:BD:BK:BI:QQ:BVT:BLT	2|1:FN:am:d1_5,i1_5:.:INDEL:hetalt	0/1:FP:am:d1_5:100:INDEL:het 	yes	no		no	yes	illumina is half 1bp ins and half 1bp del so likely an error in 2bp ins call due to noise in HiFi data on each haplotype																											19:1193449	1193450
Common		GRCh37			19	chr19	1193449	1193450	0	FP_FN	CA	C,CAAA	GT:BD:BK:BI:BVT:BLT:QQ	2|1:FN:am:d1_5,i1_5:INDEL:hetalt:.	0/1:FP:am:d1_5:INDEL:het:100	CommonFP_FN			no	yes	illumina is half 1bp ins and half 1bp del so likely an error in 2bp ins call due to noise in HiFi data on each haplotype													2|1:FN:am:d1_5,i1_5:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:18.8	2|1:FN:am:d1_5,i1_5:INDEL:hetalt:.	1/1:FP:am:d1_5:INDEL:homalt:319.73	2|1:FN:.:d1_5,i1_5:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:0	2|1:FN:am:d1_5,i1_5:INDEL:hetalt:.	0/1:FP:am:d1_5:INDEL:het:117.06	2|1:FN:am:d1_5,i1_5:INDEL:hetalt:.	0/1:FP:am:d1_5:INDEL:het:0	2|1:FN:am:d1_5,i1_5:INDEL:hetalt:.	0/1:FP:am:d1_5:INDEL:het:184.46	2|1:FN:.:d1_5,i1_5:INDEL:hetalt:.	.:.:.:.:NOCALL:nocall:0	19:1193449	1193450
Common		GRCh38			19	chr19	1193449	1193450	1	FP_FN	CA	C,CAAA	GT:BD:BK:BI:QQ:BVT:BLT	2|1:FN:am:d1_5,i1_5:.:INDEL:hetalt	0/1:FP:am:d1_5:100:INDEL:het	CommonFP_FN			no	yes	illumina is half 1bp ins and half 1bp del so likely an error in 2bp ins call due to noise in HiFi data on each haplotype													2|1:FN:am:d1_5,i1_5:.:INDEL:hetalt	.:.:.:.:18.8:NOCALL:nocall	2|1:FN:am:d1_5,i1_5:.:INDEL:hetalt	0/1:FP:am:d1_5:336.73:INDEL:het	2|1:FN:.:d1_5,i1_5:.:INDEL:hetalt	.:.:.:.:0:NOCALL:nocall	2|1:FN:am:d1_5,i1_5:.:INDEL:hetalt	0/1:FP:am:d1_5:150.06:INDEL:het	2|1:FN:am:d1_5,i1_5:.:INDEL:hetalt	0/1:FP:am:d1_5:0:INDEL:het	2|1:FN:am:d1_5,i1_5:.:INDEL:hetalt	0/1:FP:am:d1_5:184.45:INDEL:het	2|1:FN:.:d1_5,i1_5:.:INDEL:hetalt	.:.:.:.:0:NOCALL:nocall		1193449
Common		GRCh38			19	chr19	1193450	1193451	33451	FP	A	AA	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:lm:i1_5:INDEL:het	CommonFP			no	yes	illumina is half 1bp ins and half 1bp del so likely an error in 2bp ins call due to noise in HiFi data on each haplotype													./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:336.73:FP:lm:i1_5:INDEL:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:150.06:FP:lm:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:lm:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:184.45:FP:lm:i1_5:INDEL:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.		1193450
ITER	ITERteam_small-variation_GRCh37_ILMN-PB-ONT.vcf.gz	GRCh37	small-variants	SNP	19	chr19	1226901	1226902	1218350	FP_FN	G	T	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:tv:SNP:homalt	0/1:FP:am:718.93:tv:SNP:het	Yes	No																															19:1226901	1226902
Common		GRCh37			19	chr19	2445250	2445252	0	FN	G	GC	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			unsure		probably a hifiasm error in short C homopolymer but some illumina reads noisy too													0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	19:2445250	2445252
Common		GRCh38			19	chr19	2445250	2445252	1143388	FN	G	GC	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			unsure		probably a hifiasm error in short C homopolymer but some illumina reads noisy too													0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0		2445250
Common		GRCh37			19	chr19	3588638	3588640	0	FN	C	CA	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no		hifiasm error in long homopolymer likely due to noisy HiFi reads													0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	19:3588638	3588640
Common		GRCh38			19	chr19	3588638	3588640	12186	FN	C	CA	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no		hifiasm error in long homopolymer likely due to noisy HiFi reads													0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0		3588638
Roche	RN_HG002_Illumina_PacBio_Oxford_GRCh37.vcf.gz	GRCh37	small-variants	INDEL	19	chr19	3600824	3600826	0	FN	G	GT	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0 	unsure		suspicious to me. Mainly supported by PacBio, but ILM which is more accurate for homopolymers does not support it even in reads that span the homopolymers region	no		hifiasm error in long homopolymer likely due to noisy HiFi reads																											19:3600824	3600826
Common		GRCh37			19	chr19	3600824	3600826	0	FN	G	GT	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no		hifiasm error in long homopolymer likely due to noisy HiFi reads													1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	19:3600824	3600826
Common		GRCh38			19	chr19	3600824	3600826	2435023	FN	G	GT	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no		hifiasm error in long homopolymer likely due to noisy HiFi reads													1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0		3600824
Common		GRCh37			19	chr19	6035860	6035849	130431	FP	G	GT	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:40:FP:lm:i1_5:INDEL:het	CommonFP			no	yes	hifiasm miscalls length of diTR due to noisy reads													.:.:.:.:.:NOCALL:nocall	0/1:739.73:FP:lm:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:576.73:FP:lm:i1_5:INDEL:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:195.64:FP:lm:i1_5:INDEL:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:45.52:FP:lm:i1_5:INDEL:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	19:6035860	6035849
Common		GRCh37			19	chr19	6166291	6166280	0	FP	TTGTGTGTGTGTGTGTGTGTG	T	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:lm:d16_plus:INDEL:het	CommonFP			no	yes	hifiasm miscalls compound het del in diTR, likely due to homozygous region													.:.:.:.:.:NOCALL:nocall	0/1:1553.73:FP:lm:d16_plus:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:1749.73:FP:lm:d16_plus:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:lm:d16_plus:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:985.06:FP:lm:d16_plus:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:lm:d16_plus:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:151.93:FP:lm:d16_plus:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:7:FP:lm:d16_plus:INDEL:het	19:6166291	6166280
Common		GRCh38			19	chr19	6166291	6166280	16	FP	TTGTGTGTGTGTGTGTGTGTG	T	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:lm:d16_plus:INDEL:het	CommonFP			no	yes	hifiasm miscalls compound het del in diTR, likely due to homozygous region													.:.:.:.:.:NOCALL:nocall	0/1:1553.73:FP:lm:d16_plus:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:1780.73:FP:lm:d16_plus:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:lm:d16_plus:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:1522.06:FP:lm:d16_plus:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:lm:d16_plus:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:151.92:FP:lm:d16_plus:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:7:FP:lm:d16_plus:INDEL:het		6166291
Roche	RN_HG002_Illumina_PacBio_Oxford_GRCh37.vcf.gz	GRCh37	small-variants	INDEL	19	chr19	6166307	6166296	0	FP	GTGTG	G	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:lm:d1_5:INDEL:het 	no	yes	from ILM, 10X and PB, it seems that there are two alleleles one is 100bp deletion, and one 4bp deletion	no	yes	hifiasm miscalls compound het del in diTR, likely due to homozygous region																											19:6166307	6166296
Common		GRCh37			19	chr19	6166307	6166296	0	FP	GTGTG	G	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:lm:d1_5:INDEL:het	CommonFP			no	yes	hifiasm miscalls compound het del in diTR, likely due to homozygous region													.:.:.:.:.:NOCALL:nocall	0/1:1553.73:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:1749.73:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:985.06:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:151.93:FP:lm:d1_5:INDEL:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	19:6166307	6166296
Common		GRCh38			19	chr19	6166307	6166296	28	FP	GTGTG	G	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:lm:d1_5:INDEL:het	CommonFP			no	yes	hifiasm miscalls compound het del in diTR, likely due to homozygous region													.:.:.:.:.:NOCALL:nocall	0/1:1553.73:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:1780.73:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:1522.06:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:151.92:FP:lm:d1_5:INDEL:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.		6166307
BCM-HGSC_xAtlas	HG002.hs37d5.60x.1_merged.vcf.gz	GRCh37	small-variants	INDEL	19	chr19	6166335	6166324	0	FN	GTGTGTGT	G	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:lm:d6_15:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0 	Unsure	No	Illumina 60x and PacBio Sequel II alignments suggest possible TTGTGTGTGTGTGTGTGTGTG->T,TTGTGTGTGTGTGTGTG at chr19:6166291 (anchor position variable, within region of (TG)n simple repeat).	no	no	hifiasm miscalls compound het del in diTR, likely due to homozygous region																											19:6166335	6166324
Common		GRCh37			19	chr19	6166335	6166324	0	FN	GTGTGTGT	G	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:lm:d6_15:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no	yes	hifiasm miscalls compound het del in diTR, likely due to homozygous region													1|1:FN:lm:d6_15:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:lm:d6_15:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:lm:d6_15:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:lm:d6_15:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:lm:d6_15:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:lm:d6_15:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:lm:d6_15:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	19:6166335	6166324
Common		GRCh38			19	chr19	6166335	6166324	7613	FN	GTGTGTGT	G	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:lm:d6_15:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no	yes	hifiasm miscalls compound het del in diTR, likely due to homozygous region													1|1:FN:lm:d6_15:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:lm:d6_15:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:lm:d6_15:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:lm:d6_15:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:lm:d6_15:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:lm:d6_15:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:lm:d6_15:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0		6166335
NYGC	HG-002-2x250-b37.recalibrated.haplotypeCalls.vcf.gz	GRCh37	small-variants	INDEL	19	chr19	6173948	6173937	0	FP_FN	AT	A	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:115.73:d1_5:INDEL:het 	unsure	yes	There is evidence for reference allele on all the platforms. The hom-alt call is only see in Pacbio Hifi assembly.	no	yes	hifiasm misses reference haplotype in homopolymer, likely due to homozygous region																											19:6173948	6173937
Common		GRCh37			19	chr19	6173948	6173937	0	FP_FN	AT	A	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:100:d1_5:INDEL:het	CommonFP_FN			no	yes	hifiasm misses reference haplotype in homopolymer, likely due to homozygous region													1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:192.73:d1_5:INDEL:het	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:115.73:d1_5:INDEL:het	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:30:d1_5:INDEL:het	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:106.6:d1_5:INDEL:het	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:0:d1_5:INDEL:het	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:47.64:d1_5:INDEL:het	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:6:d1_5:INDEL:het	19:6173948	6173937
DNAnexus	GRCh38_HG002_WGS_union.vcf.gz	GRCh38	small-variants	INDEL	19	chr19	6173948	6173937	0	FP_FN	AT	A	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:0:d1_5:INDEL:het 	no	yes	The coverage of all sequencing technology sources are all suggesting this is a heterozygous deletion.	no	yes	hifiasm misses reference haplotype in homopolymer, likely due to homozygous region				no 	no	SINE, homopolymer T.   It looks like this is either REF or 1 (ILMN, 10X) or 2 bp (Hifi, ONT-messy) deletion. I would call this a HET.   nearby variant (6173926) does not appear to have support in data. Unsure about directly adjacent variant. 																						6173948
Common		GRCh38			19	chr19	6173948	6173937	7876	FP_FN	AT	A	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:100:d1_5:INDEL:het	CommonFP_FN			no	yes	hifiasm misses reference haplotype in homopolymer, likely due to homozygous region													1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:192.73:d1_5:INDEL:het	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:128.73:d1_5:INDEL:het	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:30:d1_5:INDEL:het	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:116.6:d1_5:INDEL:het	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:0:d1_5:INDEL:het	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:47.64:d1_5:INDEL:het	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:6:d1_5:INDEL:het		6173948
Common		GRCh38			19	chr19	6181824	6181813	507509	FP_FN	G	GCC,GCCCC,GCCCCC	GT:BD:BK:QQ:BI:BVT:BLT	3|3:FN:lm:.:i1_5:INDEL:homalt	2/1:FP:lm:100:i1_5:INDEL:hetalt	CommonFP_FN			unsure	unsure	long C homopolymer in homozygous region that is noisy across techs and illumina reads have C systematic errors after homopolymer													3|3:FN:lm:.:i1_5:INDEL:homalt	2/2:FP:lm:1434.73:i1_5:INDEL:homalt	3|3:FN:lm:.:i1_5:INDEL:homalt	2/2:FP:lm:175.73:i1_5:INDEL:homalt	3|3:FN:am:.:i1_5:INDEL:homalt	3/1:FP:am:30:i1_5:INDEL:hetalt	3|3:FN:.:.:i1_5:INDEL:homalt	.:.:.:0:.:NOCALL:nocall	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	3|3:FN:lm:.:i1_5:INDEL:homalt	2/1:FP:lm:102.74:i1_5:INDEL:hetalt	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.		6181824
Common		GRCh37			19	chr19	6689333	6689322	13	FN	TACCTAC	T	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:lm:d6_15:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	benchmark supported by illumina, though few reads cross repetitive region													1|0:TP:gm:d6_15:INDEL:het:224.73	0/1:TP:gm:d6_15:INDEL:het:224.73	1|0:TP:gm:d6_15:INDEL:het:613.73	0/1:TP:gm:d6_15:INDEL:het:613.73	1|0:FN:lm:d6_15:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:lm:d6_15:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:lm:d6_15:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:d6_15:INDEL:het:46.41	0/1:TP:gm:d6_15:INDEL:het:46.41	1|0:FN:lm:d6_15:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	19:6689333	6689322
Common		GRCh37			19	chr19	6689346	6689335	1720	FP_FN	C	A	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:tv:SNP:homalt	0/1:FP:am:30.0008:tv:SNP:het	CommonFP_FN			yes	no	benchmark supported by illumina, though few reads cross repetitive region													1|1:FN:am:.:tv:SNP:homalt	0/1:FP:am:514.77:tv:SNP:het	1|1:TP:gm:724.77:tv:SNP:homalt	1/1:TP:gm:724.77:tv:SNP:homalt	1|1:TP:gm:30:tv:SNP:homalt	1/1:TP:gm:30:tv:SNP:homalt	1|1:FN:am:.:tv:SNP:homalt	0/1:FP:am:357.81:tv:SNP:het	1|1:FN:am:.:tv:SNP:homalt	0/1:FP:am:0:tv:SNP:het	1|1:TP:gm:38.19:tv:SNP:homalt	1/1:TP:gm:38.19:tv:SNP:homalt	1|1:FN:am:.:tv:SNP:homalt	0/1:FP:am:19:tv:SNP:het	19:6689346	6689335
BCM-HGSC_xAtlas	HG002.hs37d5.60x.1_merged.vcf.gz	GRCh37	small-variants	INDEL	19	chr19	6691066	6691055	5995	FP_FN	C	CTT,CTTTTT	GT:BD:BK:BI:QQ:BVT:BLT	2|1:FN:am:i1_5:.:INDEL:hetalt	1/1:FP:am:i1_5:7:INDEL:homalt 	Yes	No																															19:6691066	6691055
PacBio_gatk4	gatk4hc_HG002_15kb_20kb_52X_SequelII.vcf.gz	GRCh37	small-variants	INDEL	19	chr19	6697061	6697050	939	FP	A	AAAT	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:517.73:FP:lm:i1_5:INDEL:het	yes	yes	equivalent representation of a complex event; both gatk and syndip represent the variant allele as AAAAAAATAATAAAAAAAT	yes	no	GATK miscalls part of complex event																											19:6697061	6697050
Roche	RN_HG002_Illumina_PacBio_Oxford_GRCh37.vcf.gz	GRCh37	small-variants	INDEL	19	chr19	6698000	6697989	6908	FP_FN	TTTATTATTATTATTA	T,TTTA	GT:BD:BK:BI:QQ:BVT:BLT	1|2:FN:am:d6_15:.:INDEL:hetalt	0/1:FP:am:d6_15:100:INDEL:het 	yes	no																															19:6698000	6697989
Common		GRCh37			19	chr19	6704908	6704897	0	FN	C	CA	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no		hifiasm error in long homopolymer likely due to noisy HiFi reads													0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	19:6704908	6704897
Common		GRCh38			19	chr19	6704908	6704897	3673936	FN	C	CA	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no		hifiasm error in long homopolymer likely due to noisy HiFi reads													0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0		6704908
DNAnexus	GRCh38_HG002_WGS_union.vcf.gz	GRCh38	small-variants	INDEL	19	chr19	10489509	10378833	5305923	FP	ATATCTTATCTTATCT	A	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:lm:d6_15:INDEL:het 	yes	yes	Both benchmark set and query callset are right. The differences is due to VCF variant record formatting.	yes	no	query misses 10bp ins on other haplotype																												10489509
Common		GRCh37			19	chr19	15795566	15684756	0	FP_FN	TTGTGTGTG	T	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:d6_15:INDEL:homalt	0/1:FP:am:100:d6_15:INDEL:het	CommonFP_FN			no		hifiasm misses haplotype in diTR due to homozygous region													1|1:FN:am:.:d6_15:INDEL:homalt	0/1:FP:am:1722.73:d6_15:INDEL:het	1|1:FN:am:.:d6_15:INDEL:homalt	0/1:FP:am:1126.73:d6_15:INDEL:het	1|1:FN:am:.:d6_15:INDEL:homalt	0/1:FP:am:30:d6_15:INDEL:het	1|1:FN:am:.:d6_15:INDEL:homalt	0/1:FP:am:762.06:d6_15:INDEL:het	1|1:TP:gm:0:d6_15:INDEL:homalt	0/1:TP:gm:0:d6_15:INDEL:het	1|1:FN:am:.:d6_15:INDEL:homalt	0/1:FP:am:180.63:d6_15:INDEL:het	1|1:FN:am:.:d6_15:INDEL:homalt	0/1:FP:am:13:d6_15:INDEL:het	19:15795566	15684756
Common		GRCh38			19	chr19	15795566	15684756	4	FP_FN	TTGTGTGTG	T	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:d6_15:INDEL:homalt	0/1:FP:am:100:d6_15:INDEL:het	CommonFP_FN			no		hifiasm misses haplotype in diTR due to homozygous region													1|1:FN:am:.:d6_15:INDEL:homalt	0/1:FP:am:1722.73:d6_15:INDEL:het	1|1:FN:am:.:d6_15:INDEL:homalt	0/1:FP:am:1130.73:d6_15:INDEL:het	1|1:FN:am:.:d6_15:INDEL:homalt	0/1:FP:am:30:d6_15:INDEL:het	1|1:FN:am:.:d6_15:INDEL:homalt	0/1:FP:am:1231.06:d6_15:INDEL:het	1|1:TP:gm:0:d6_15:INDEL:homalt	0/1:TP:gm:0:d6_15:INDEL:het	1|1:FN:am:.:d6_15:INDEL:homalt	0/1:FP:am:181.99:d6_15:INDEL:het	1|1:FN:am:.:d6_15:INDEL:homalt	0/1:FP:am:13:d6_15:INDEL:het		15795566
ITER	ITERteam_small-variation_GRCh37_ILMN-PB-ONT.vcf.gz	GRCh37	small-variants	INDEL	19	chr19	15795570	15684760	0	FP	GTGTG	G	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:762.06:FP:lm:d1_5:INDEL:het	No	Yes	We both detect two deletions of 4 and 8nt, but in truth only 8nts deletion is called.	no		hifiasm misses haplotype in diTR due to homozygous region																											19:15795570	15684760
Common		GRCh37			19	chr19	15795570	15684760	0	FP	GTGTG	G	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:lm:d1_5:INDEL:het	CommonFP			no		hifiasm misses haplotype in diTR due to homozygous region													.:.:.:.:.:NOCALL:nocall	0/1:1722.73:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:1126.73:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:762.06:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:180.63:FP:lm:d1_5:INDEL:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	19:15795570	15684760
Common		GRCh38			19	chr19	15795570	15684760	802721	FP	GTGTG	G	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:lm:d1_5:INDEL:het	CommonFP			no		hifiasm misses haplotype in diTR due to homozygous region													.:.:.:.:.:NOCALL:nocall	0/1:1722.73:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:1130.73:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:1231.06:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:181.99:FP:lm:d1_5:INDEL:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.		15795570
Common		GRCh37			19	chr19	16598292	16487481	0	FP_FN	C	CA,CAA	GT:BD:BK:QQ:BI:BVT:BLT	0|2:FN:lm:.:i1_5:INDEL:het	0/1:FP:lm:100:i1_5:INDEL:het	CommonFP_FN			no	yes	hifiasm error in long homopolymer likely due to noisy HiFi reads													0|2:FN:lm:.:i1_5:INDEL:het	.:.:.:0:.:NOCALL:nocall	0|2:FN:lm:.:i1_5:INDEL:het	0/1:FP:lm:84.89:i1_5:INDEL:het	0|2:FN:lm:.:i1_5:INDEL:het	1/1:FP:lm:30:i1_5:INDEL:homalt	0|2:FN:lm:.:i1_5:INDEL:het	0/1:FP:lm:66.64:i1_5:INDEL:het	0|2:FN:lm:.:i1_5:INDEL:het	0/1:FP:lm:0:i1_5:INDEL:het	0|2:FN:lm:.:i1_5:INDEL:het	0/1:FP:lm:50:i1_5:INDEL:het	0|2:FN:lm:.:i1_5:INDEL:het	0/1:FP:lm:11:i1_5:INDEL:het	19:16598292	16487481
Common		GRCh38			19	chr19	16598292	16487481	600449	FP_FN	C	CA,CAA	GT:BD:BK:QQ:BI:BVT:BLT	0|2:FN:lm:.:i1_5:INDEL:het	0/1:FP:lm:100:i1_5:INDEL:het	CommonFP_FN			no	yes	hifiasm error in long homopolymer likely due to noisy HiFi reads													0|2:FN:lm:.:i1_5:INDEL:het	.:.:.:0:.:NOCALL:nocall	0|2:FN:lm:.:i1_5:INDEL:het	0/1:FP:lm:99.82:i1_5:INDEL:het	0|2:FN:lm:.:i1_5:INDEL:het	1/1:FP:lm:30:i1_5:INDEL:homalt	0|2:FN:lm:.:i1_5:INDEL:het	0/1:FP:lm:61.64:i1_5:INDEL:het	0|2:FN:lm:.:i1_5:INDEL:het	0/1:FP:lm:0:i1_5:INDEL:het	0|2:FN:lm:.:i1_5:INDEL:het	0/1:FP:lm:50:i1_5:INDEL:het	0|2:FN:lm:.:i1_5:INDEL:het	0/1:FP:lm:11:i1_5:INDEL:het		16598292
ITER	ITERteam_small-variation_GRCh37_ILMN-PB-ONT.vcf.gz	GRCh37	small-variants	INDEL	19	chr19	17198740	17087930	11886	FN	C	CA	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	Yes	No																															19:17198740	17087930
Common		GRCh37			19	chr19	17210626	17099816	47726	FP	AA	A	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:lm:d1_5:INDEL:het	CommonFP			unsure	unsure	all techs noisy in T homopolymer													./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:338.06:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:123.79:FP:lm:d1_5:INDEL:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	19:17210626	17099816
Common		GRCh37			19	chr19	17258352	17147542	0	FN	C	CA	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no	yes	hifiasm error in long homopolymer likely due to noisy HiFi reads													0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	19:17258352	17147542
Common		GRCh38			19	chr19	17258352	17147542	17222162	FN	C	CA	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no	yes	hifiasm error in long homopolymer likely due to noisy HiFi reads													0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0		17258352
ITER	ITERteam_small-variation_GRCh38_ILMN-PB-ONT.vcf.gz	GRCh38	small-variants	INDEL	19	chr19	34860609	34369704	1907	FP_FN	C	CA,CAAA,CAA	GT:BD:BK:QQ:BI:BVT:BLT	3|3:FN:lm:.:i1_5:INDEL:homalt	2/1:FP:lm:10.8:i1_5:INDEL:hetalt	Yes	No	Repetitive region of polyAs. Low quality for our genotype. 2nt insertion well supported in ILMN, 10x and PacBio in truth; and ILMN and PacBio in query.	yes	no	benchmark appears supported across techs				skip																								34860609
Common		GRCh37			19	chr19	34862516	34371611	0	FP_FN	G	A	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:ti:SNP:homalt	0/1:FP:am:100:ti:SNP:het	CommonFP_FN			no	yes	benchmark misses one haplotype at SNV likely due to highly homozygous region													1|1:FN:am:.:ti:SNP:homalt	0/1:FP:am:475.77:ti:SNP:het	1|1:FN:am:.:ti:SNP:homalt	0/1:FP:am:263.77:ti:SNP:het	1|1:FN:am:.:ti:SNP:homalt	0/1:FP:am:30:ti:SNP:het	1|1:FN:am:.:ti:SNP:homalt	0/1:FP:am:267.6:ti:SNP:het	1|1:FN:am:.:ti:SNP:homalt	0/1:FP:am:0:ti:SNP:het	1|1:FN:am:.:ti:SNP:homalt	0/1:FP:am:50:ti:SNP:het	1|1:FN:am:.:ti:SNP:homalt	0/1:FP:am:35:ti:SNP:het	19:34862516	34371611
Common		GRCh38			19	chr19	34862516	34371611	6586	FP_FN	G	A	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:ti:SNP:homalt	0/1:FP:am:100:ti:SNP:het	CommonFP_FN			no	yes	benchmark misses one haplotype at SNV likely due to highly homozygous region													1|1:FN:am:.:ti:SNP:homalt	0/1:FP:am:475.77:ti:SNP:het	1|1:FN:am:.:ti:SNP:homalt	0/1:FP:am:257.77:ti:SNP:het	1|1:FN:am:.:ti:SNP:homalt	0/1:FP:am:30:ti:SNP:het	1|1:FN:am:.:ti:SNP:homalt	0/1:FP:am:24.4:ti:SNP:het	1|1:FN:am:.:ti:SNP:homalt	0/1:FP:am:0:ti:SNP:het	1|1:FN:am:.:ti:SNP:homalt	0/1:FP:am:50:ti:SNP:het	1|1:FN:am:.:ti:SNP:homalt	0/1:FP:am:35:ti:SNP:het		34862516
Common		GRCh37			19	chr19	34869102	34378197	0	FP_FN	CTTG	C	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:100:d1_5:INDEL:het	CommonFP_FN			no	yes	benchmark misses one haplotype at TR likely due to highly homozygous region													1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:531.73:d1_5:INDEL:het	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:928.73:d1_5:INDEL:het	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:30:d1_5:INDEL:het	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:397.6:d1_5:INDEL:het	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:0:d1_5:INDEL:het	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:48.97:d1_5:INDEL:het	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:10:d1_5:INDEL:het	19:34869102	34378197
NYGC	HG-002-2x250-b38.recalibrated.haplotypeCalls.vcf.gz	GRCh38	small-variants	INDEL	19	chr19	34869102	34378197	0	FP_FN	CTTG	C	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:479.73:d1_5:INDEL:het 	yes	yes		no	yes	benchmark misses one haplotype at TR likely due to highly homozygous region																												34869102
Common		GRCh38			19	chr19	34869102	34378197	6516811	FP_FN	CTTG	C	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:100:d1_5:INDEL:het	CommonFP_FN			no	yes	benchmark misses one haplotype at TR likely due to highly homozygous region													1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:531.73:d1_5:INDEL:het	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:479.73:d1_5:INDEL:het	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:30:d1_5:INDEL:het	1|1:FN:.:.:d1_5:INDEL:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:0:d1_5:INDEL:het	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:48.97:d1_5:INDEL:het	1|1:FN:am:.:d1_5:INDEL:homalt	0/1:FP:am:10:d1_5:INDEL:het		34869102
DNAnexus	GRCh38_HG002_WGS_union.vcf.gz	GRCh38	small-variants	INDEL	19	chr19	41400913	40895008	15918	FN	AAAAC	A	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0 	yes	no	The variant is called by all short-read variant callers. It didn't get included in the VCF because the variant representation formatting issue.							skip																								41400913
Common		GRCh38			19	chr19	41416831	40910926	2597420	FP	AT	A	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:.:d1_5:INDEL:het	CommonFP			no	yes	benchmark misses one haplotype at homopolymer likely due to highly homozygous region													.:.:.:.:.:NOCALL:nocall	0/1:482.73:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:356.73:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:.:d1_5:INDEL:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:50:FP:.:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:10:FP:.:d1_5:INDEL:het		41416831
Common		GRCh37			19	chr19	44012498	43508346	6139	FP_FN	C	CTT,CTTTTT	GT:BD:BK:BI:QQ:BVT:BLT	1|2:FN:.:i1_5:.:INDEL:hetalt	.:.:.:.:0:NOCALL:nocall	CommonFP_FN			yes	no	benchmark supported by illumina in long homopolymer													1|2:FN:am:i1_5:.:INDEL:hetalt	0/2:FP:am:i1_5:606.73:INDEL:het	1|2:FN:am:i1_5:.:INDEL:hetalt	1/1:FP:am:i1_5:362.73:INDEL:homalt	1|2:FN:am:i1_5:.:INDEL:hetalt	2/2:FP:am:i1_5:30:INDEL:homalt	1|2:FN:am:i1_5:.:INDEL:hetalt	1/1:FP:am:i1_5:178.02:INDEL:homalt	1|2:TP:gm:i1_5:0:INDEL:hetalt	0/1:TP:gm:i1_5:0:INDEL:het	1|2:TP:gm:i1_5:263.34:INDEL:hetalt	2/1:TP:gm:i1_5:263.34:INDEL:hetalt	1|2:FN:am:i1_5:.:INDEL:hetalt	1/1:FP:am:i1_5:8:INDEL:homalt	19:44012498	43508346
NCBI	HG002_grch37_dipcall.vcf.gz	GRCh37	small-variants	INDEL	19	chr19	44018637	43514485	0	FP_FN	C	CTTT,CTTTT	GT:BD:BK:QQ:BI:BVT:BLT	0|2:FN:lm:.:i1_5:INDEL:het	0/1:FP:lm:30:i1_5:INDEL:het	unsure	unsure	evidence for 3T-7T INS here; repeat region	no	yes	hifiasm error in long homopolymer likely due to noisy HiFi reads																											19:44018637	43514485
Common		GRCh38			19	chr19	44018637	43514485	1401652	FP_FN	C	CTTT,CTTTT	GT:BD:BK:QQ:BI:BVT:BLT	0|2:FN:lm:.:i1_5:INDEL:het	0/1:FP:lm:36.9903:i1_5:INDEL:het	CommonFP_FN			no	yes	hifiasm error in long homopolymer likely due to noisy HiFi reads													0|2:FN:.:.:i1_5:INDEL:het	.:.:.:0:.:NOCALL:nocall	0|2:FN:lm:.:i1_5:INDEL:het	0/1:FP:lm:60.73:i1_5:INDEL:het	0|2:FN:lm:.:i1_5:INDEL:het	0/1:FP:lm:30:i1_5:INDEL:het	0|2:FN:lm:.:i1_5:INDEL:het	0/1:FP:lm:125.64:i1_5:INDEL:het	0|2:FN:.:.:i1_5:INDEL:het	.:.:.:0:.:NOCALL:nocall	0|2:FN:lm:.:i1_5:INDEL:het	0/1:FP:lm:48.41:i1_5:INDEL:het	0|2:FN:.:.:i1_5:INDEL:het	.:.:.:0:.:NOCALL:nocall		44018637
Common		GRCh37			19	chr19	45419394	44916137	0	FP_FN	C	CAAAAAAAA,CAAAAAAAAAA,CAAAAAAAAA	GT:BD:BK:BI:QQ:BVT:BLT	2|1:FN:lm:i6_15:.:INDEL:hetalt	3/3:FP:lm:i6_15:100:INDEL:homalt	CommonFP_FN			unsure	unsure	large ins in long homopolymer, and hifi looks slightly different between haplotypes													2|1:FN:.:i6_15:.:INDEL:hetalt	.:.:.:.:0:NOCALL:nocall	2|1:FN:.:i6_15:.:INDEL:hetalt	.:.:.:.:0:NOCALL:nocall	2|1:FN:lm:i6_15:.:INDEL:hetalt	3/3:FP:lm:i6_15:30:INDEL:homalt	2|1:FN:am:i6_15:.:INDEL:hetalt	1/1:FP:am:i6_15:234.53:INDEL:homalt	2|1:FN:am:i6_15:.:INDEL:hetalt	1/1:FP:am:i6_15:0:INDEL:homalt	2|1:FN:am:i6_15:.:INDEL:hetalt	3/1:FP:am:i6_15:104.94:INDEL:hetalt	2|1:FN:am:i6_15:.:INDEL:hetalt	1/1:FP:am:i6_15:14:INDEL:homalt	19:45419394	44916137
Common		GRCh38			19	chr19	45419394	44916137	290284	FP_FN	C	CAAAAAAAAA,CAAAAAAAA,CAAAAAAAAAA	GT:BD:BK:QQ:BI:BVT:BLT	3|2:FN:lm:.:i6_15:INDEL:hetalt	1/1:FP:lm:100:i6_15:INDEL:homalt	CommonFP_FN			unsure	unsure	large ins in long homopolymer, and hifi looks slightly different between haplotypes													3|2:FN:.:.:i6_15:INDEL:hetalt	.:.:.:0:.:NOCALL:nocall	3|2:FN:.:.:i6_15:INDEL:hetalt	.:.:.:0:.:NOCALL:nocall	3|2:FN:lm:.:i6_15:INDEL:hetalt	1/1:FP:lm:30:i6_15:INDEL:homalt	3|2:FN:am:.:i6_15:INDEL:hetalt	3/3:FP:am:76.96:i6_15:INDEL:homalt	3|2:FN:am:.:i6_15:INDEL:hetalt	2/2:FP:am:0:i6_15:INDEL:homalt	3|2:FN:am:.:i6_15:INDEL:hetalt	1/2:FP:am:103.79:i6_15:INDEL:hetalt	3|2:FN:am:.:i6_15:INDEL:hetalt	2/2:FP:am:14:i6_15:INDEL:homalt		45419394
Common		GRCh38			19	chr19	45709679	45206421	567841	FN	CTT	C	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no	yes	looks like hifiasm consensus error since no support in reads from any tech													1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0		45709679
BCM-HGSC_xAtlas	HG002.hs37d5.60x.1_merged.vcf.gz	GRCh37	small-variants	INDEL	19	chr19	46277520	45774262	0	FP_FN	C	CT,CTT	GT:BD:BK:QQ:BI:BVT:BLT	2|2:FN:lm:.:i1_5:INDEL:homalt	1/1:FP:lm:10:i1_5:INDEL:homalt 	Yes	No		no	yes	benchmark calls homvar instead of 1/2bp ins in long homopolymer																											19:46277520	45774262
Common		GRCh37			19	chr19	46277520	45774262	4087470	FP_FN	C	CT,CTT	GT:BD:BK:QQ:BI:BVT:BLT	2|2:FN:am:.:i1_5:INDEL:homalt	2/1:FP:am:100:i1_5:INDEL:hetalt	CommonFP_FN			no	yes	benchmark calls homvar instead of 1/2bp ins in long homopolymer													2|2:TP:gm:286.73:i1_5:INDEL:homalt	2/2:TP:gm:286.73:i1_5:INDEL:homalt	2|2:FN:am:.:i1_5:INDEL:homalt	2/1:FP:am:828.73:i1_5:INDEL:hetalt	2|2:FN:am:.:i1_5:INDEL:homalt	2/1:FP:am:30:i1_5:INDEL:hetalt	2|2:FN:am:.:i1_5:INDEL:homalt	2/1:FP:am:219.1:i1_5:INDEL:hetalt	2|2:FN:am:.:i1_5:INDEL:homalt	2/1:FP:am:0:i1_5:INDEL:hetalt	2|2:FN:am:.:i1_5:INDEL:homalt	2/1:FP:am:171.65:i1_5:INDEL:hetalt	2|2:FN:lm:.:i1_5:INDEL:homalt	1/1:FP:lm:10:i1_5:INDEL:homalt	19:46277520	45774262
BCM-HGSC_xAtlas	HG002.GRCh38.60x.1_merged.vcf.gz	GRCh38	small-variants	SNP	19	chr19	50364989	49861732	108440	FP	A	C	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:3:FP:.:tv:SNP:het 	Yes	No								skip																								50364989
Common		GRCh37			19	chr19	50473429	49970172	19	FN	A	ATGCG	GT:BD:BK:BI:BVT:BLT:QQ	1|0:TP:gm:i1_5:INDEL:het:10.0601	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	Dense region of variants on one haplotype in SIGLEC16, possibly related to past gene conversions with nearby SIGLEC11, which causes short reads to miss one haplotype													1|0:TP:gm:i1_5:INDEL:het:796.73	.:.:.:.:NOCALL:nocall:0	1|0:FN:lm:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:i1_5:INDEL:het:30	0/1:TP:gm:i1_5:INDEL:het:30	1|0:FN:lm:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:lm:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:lm:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:lm:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	19:50473429	49970172
Common		GRCh37			19	chr19	50473448	49970191	0	FP_FN	G	C	GT:BD:BK:QQ:BI:BVT:BLT	0|1:TP:gm:36.989:tv:SNP:het	0/1:TP:gm:36.989:tv:SNP:het	CommonFP_FN			yes	no	Dense region of variants on one haplotype in SIGLEC16, possibly related to past gene conversions with nearby SIGLEC11, which causes short reads to miss one haplotype													0|1:TP:gm:580.77:tv:SNP:het	0/1:TP:gm:580.77:tv:SNP:het	0|1:FN:am:.:tv:SNP:het	1/1:FP:am:514.77:tv:SNP:homalt	0|1:TP:gm:30:tv:SNP:het	0/1:TP:gm:30:tv:SNP:het	0|1:FN:am:.:tv:SNP:het	1/1:FP:am:428.02:tv:SNP:homalt	0|1:FN:am:.:tv:SNP:het	1/1:FP:am:0:tv:SNP:homalt	0|1:FN:am:.:tv:SNP:het	1/1:FP:am:84.89:tv:SNP:homalt	0|1:FN:am:.:tv:SNP:het	1/1:FP:am:35:tv:SNP:homalt	19:50473448	49970191
DNAnexus	GRCh38_HG002_WGS_union.vcf.gz	GRCh38	small-variants	SNP	19	chr19	50473448	49970191	0	FP_FN	G	C	GT:BD:BK:QQ:BI:BVT:BLT	0|1:FN:am:.:tv:SNP:het	1/1:FP:am:0:tv:SNP:homalt 	yes	no		yes	no	Dense region of variants on one haplotype in SIGLEC16, possibly related to past gene conversions with nearby SIGLEC11, which causes short reads to miss one haplotype				skip																								50473448
Common		GRCh38			19	chr19	50473448	49970191	113	FP_FN	G	C	GT:BD:BK:QQ:BI:BVT:BLT	0|1:TP:gm:36.989:tv:SNP:het	0/1:TP:gm:36.989:tv:SNP:het	CommonFP_FN			yes	no	Dense region of variants on one haplotype in SIGLEC16, possibly related to past gene conversions with nearby SIGLEC11, which causes short reads to miss one haplotype													0|1:TP:gm:580.77:tv:SNP:het	0/1:TP:gm:580.77:tv:SNP:het	0|1:FN:am:.:tv:SNP:het	1/1:FP:am:631.77:tv:SNP:homalt	0|1:TP:gm:30:tv:SNP:het	0/1:TP:gm:30:tv:SNP:het	0|1:FN:am:.:tv:SNP:het	1/1:FP:am:724.03:tv:SNP:homalt	0|1:FN:am:.:tv:SNP:het	1/1:FP:am:0:tv:SNP:homalt	0|1:FN:am:.:tv:SNP:het	1/1:FP:am:84.89:tv:SNP:homalt	0|1:FN:am:.:tv:SNP:het	1/1:FP:am:35:tv:SNP:homalt		50473448
Common		GRCh37			19	chr19	50473561	49970304	0	FN	AC	A	GT:BD:BK:BI:BVT:BLT:QQ	1|0:TP:gm:d1_5:INDEL:het:100	0/1:TP:gm:d1_5:INDEL:het:100	CommonFN			yes	no	Dense region of variants on one haplotype in SIGLEC16, possibly related to past gene conversions with nearby SIGLEC11, which causes short reads to miss one haplotype													1|0:TP:gm:d1_5:INDEL:het:709.73	0/1:TP:gm:d1_5:INDEL:het:709.73	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:d1_5:INDEL:het:30	0/1:TP:gm:d1_5:INDEL:het:30	1|0:FN:lm:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	19:50473561	49970304
DNAnexus	GRCh38_HG002_WGS_union.vcf.gz	GRCh38	small-variants	INDEL	19	chr19	50473561	49970304	0	FN	AC	A	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0 	yes	no	PacBio data suggested there is a heterozygous deletion. ONT data kind of support this deletion. Short read (illumiina and 10x) didn't have information supporting this variants.	yes	no	Dense region of variants on one haplotype in SIGLEC16, possibly related to past gene conversions with nearby SIGLEC11, which causes short reads to miss one haplotype				skip																								50473561
Common		GRCh38			19	chr19	50473561	49970304	663	FN	AC	A	GT:BD:BK:QQ:BI:BVT:BLT	1|0:TP:gm:100:d1_5:INDEL:het	0/1:TP:gm:100:d1_5:INDEL:het	CommonFN			yes	no	Dense region of variants on one haplotype in SIGLEC16, possibly related to past gene conversions with nearby SIGLEC11, which causes short reads to miss one haplotype													1|0:TP:gm:709.73:d1_5:INDEL:het	0/1:TP:gm:709.73:d1_5:INDEL:het	1|0:FN:.:.:d1_5:INDEL:het	.:.:.:0:.:NOCALL:nocall	1|0:TP:gm:30:d1_5:INDEL:het	0/1:TP:gm:30:d1_5:INDEL:het	1|0:FN:lm:.:d1_5:INDEL:het	.:.:.:0:.:NOCALL:nocall	1|0:FN:.:.:d1_5:INDEL:het	.:.:.:0:.:NOCALL:nocall	1|0:FN:.:.:d1_5:INDEL:het	.:.:.:0:.:NOCALL:nocall	1|0:FN:.:.:d1_5:INDEL:het	.:.:.:0:.:NOCALL:nocall		50473561
NCBI	HG002_grch37_dipcall.vcf.gz	GRCh37	small-variants	SNP	19	chr19	50474224	49970967	102	FP_FN	G	A	GT:BD:BK:QQ:BI:BVT:BLT	1|0:FN:am:.:ti:SNP:het	1/1:FP:am:30:ti:SNP:homalt	yes	no	evidence for HET; segdup 	yes	no	Dense region of variants on one haplotype in SIGLEC16, possibly related to past gene conversions with nearby SIGLEC11, which causes short reads to miss one haplotype																											19:50474224	49970967
BCM-HGSC_xAtlas	HG002.hs37d5.60x.1_merged.vcf.gz	GRCh37	small-variants	SNP	19	chr19	50474326	49971069	29	FN	T	C	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:lm:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0 	Yes	No		yes	no	Dense region of variants on one haplotype in SIGLEC16, possibly related to past gene conversions with nearby SIGLEC11, which causes short reads to miss one haplotype																											19:50474326	49971069
NCBI	HG002_grch38_dipcall.vcf.gz	GRCh38	small-variants	INDEL	19	chr19	50474355	49971098	194	FN	CCTCT	C	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:lm:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	yes	no	segdup region	yes	no	Dense region of variants on one haplotype in SIGLEC16, possibly related to past gene conversions with nearby SIGLEC11, which causes short reads to miss one haplotype				skip																								50474355
CMH_DRAGEN_3.6.3	NA24385.hard-filtered.vcf.gz	GRCh37	small-variants	SNP	19	chr19	50474549	49971292	0	FP_FN	G	C	GT:BD:BK:QQ:BI:BVT:BLT	1|0:FN:am:.:tv:SNP:het	1/1:FP:am:51.63:tv:SNP:homalt	yes	no		yes	no	Dense region of variants on one haplotype in SIGLEC16, possibly related to past gene conversions with nearby SIGLEC11, which causes short reads to miss one haplotype																											19:50474549	49971292
CMH_DRAGEN_3.6.3	NA24385.hard-filtered.vcf.gz	GRCh38	small-variants	SNP	19	chr19	50474549	49971292	13	FP_FN	G	C	GT:BD:BK:QQ:BI:BVT:BLT	1|0:FN:am:.:tv:SNP:het	1/1:FP:am:51.63:tv:SNP:homalt	yes	no		yes	no	Dense region of variants on one haplotype in SIGLEC16, possibly related to past gene conversions with nearby SIGLEC11, which causes short reads to miss one haplotype				skip																								50474549
NCBI	HG002_grch38_dipcall.vcf.gz	GRCh38	small-variants	SNP	19	chr19	50474562	49971305	289	FP_FN	C	T	GT:BD:BK:QQ:BI:BVT:BLT	1|0:FN:am:.:ti:SNP:het	1/1:FP:am:30:ti:SNP:homalt	yes	no	most likely hst; segdup	yes	no	Dense region of variants on one haplotype in SIGLEC16, possibly related to past gene conversions with nearby SIGLEC11, which causes short reads to miss one haplotype				skip																								50474562
Common		GRCh37			19	chr19	50474851	49971594	0	FN	C	G	GT:BD:BK:BI:BVT:BLT:QQ	0|1:TP:gm:tv:SNP:het:100	0/1:TP:gm:tv:SNP:het:100	CommonFN			yes	no	Dense region of variants on one haplotype in SIGLEC16, possibly related to past gene conversions with nearby SIGLEC11, which causes short reads to miss one haplotype													0|1:TP:gm:tv:SNP:het:703.77	0/1:TP:gm:tv:SNP:het:703.77	0|1:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:TP:gm:tv:SNP:het:41.7	0/1:TP:gm:tv:SNP:het:41.7	0|1:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	19:50474851	49971594
Common		GRCh38			19	chr19	50474851	49971594	8	FN	C	G	GT:BD:BK:QQ:BI:BVT:BLT	0|1:TP:gm:100:tv:SNP:het	0/1:TP:gm:100:tv:SNP:het	CommonFN			yes	no	Dense region of variants on one haplotype in SIGLEC16, possibly related to past gene conversions with nearby SIGLEC11, which causes short reads to miss one haplotype													0|1:TP:gm:703.77:tv:SNP:het	0/1:TP:gm:703.77:tv:SNP:het	0|1:FN:.:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:.:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:TP:gm:40.3:tv:SNP:het	0/1:TP:gm:40.3:tv:SNP:het	0|1:FN:.:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:.:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:.:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall		50474851
Common		GRCh37			19	chr19	50474859	49971602	0	FN	C	T	GT:BD:BK:BI:BVT:BLT:QQ	0|1:TP:gm:ti:SNP:het:100	0/1:TP:gm:ti:SNP:het:100	CommonFN			yes	no	Dense region of variants on one haplotype in SIGLEC16, possibly related to past gene conversions with nearby SIGLEC11, which causes short reads to miss one haplotype													0|1:TP:gm:ti:SNP:het:703.77	0/1:TP:gm:ti:SNP:het:703.77	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:TP:gm:ti:SNP:het:18.9	0/1:TP:gm:ti:SNP:het:18.9	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	19:50474859	49971602
Common		GRCh38			19	chr19	50474859	49971602	1	FN	C	T	GT:BD:BK:QQ:BI:BVT:BLT	0|1:TP:gm:100:ti:SNP:het	0/1:TP:gm:100:ti:SNP:het	CommonFN			yes	no	Dense region of variants on one haplotype in SIGLEC16, possibly related to past gene conversions with nearby SIGLEC11, which causes short reads to miss one haplotype													0|1:TP:gm:703.77:ti:SNP:het	0/1:TP:gm:703.77:ti:SNP:het	0|1:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:TP:gm:17.1:ti:SNP:het	0/1:TP:gm:17.1:ti:SNP:het	0|1:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall		50474859
Common		GRCh37			19	chr19	50474860	49971603	0	FN	G	A	GT:BD:BK:BI:BVT:BLT:QQ	0|1:TP:gm:ti:SNP:het:100	0/1:TP:gm:ti:SNP:het:100	CommonFN			yes	no	Dense region of variants on one haplotype in SIGLEC16, possibly related to past gene conversions with nearby SIGLEC11, which causes short reads to miss one haplotype													0|1:TP:gm:ti:SNP:het:703.77	0/1:TP:gm:ti:SNP:het:703.77	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:TP:gm:ti:SNP:het:16.4	0/1:TP:gm:ti:SNP:het:16.4	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	19:50474860	49971603
Common		GRCh38			19	chr19	50474860	49971603	1	FN	G	A	GT:BD:BK:QQ:BI:BVT:BLT	0|1:TP:gm:100:ti:SNP:het	0/1:TP:gm:100:ti:SNP:het	CommonFN			yes	no	Dense region of variants on one haplotype in SIGLEC16, possibly related to past gene conversions with nearby SIGLEC11, which causes short reads to miss one haplotype													0|1:TP:gm:703.77:ti:SNP:het	0/1:TP:gm:703.77:ti:SNP:het	0|1:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:TP:gm:14.3:ti:SNP:het	0/1:TP:gm:14.3:ti:SNP:het	0|1:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall		50474860
Common		GRCh37			19	chr19	50474861	49971604	0	FN	C	G	GT:BD:BK:BI:BVT:BLT:QQ	0|1:TP:gm:tv:SNP:het:100	0/1:TP:gm:tv:SNP:het:100	CommonFN			yes	no	Dense region of variants on one haplotype in SIGLEC16, possibly related to past gene conversions with nearby SIGLEC11, which causes short reads to miss one haplotype													0|1:TP:gm:tv:SNP:het:703.77	0/1:TP:gm:tv:SNP:het:703.77	0|1:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:TP:gm:tv:SNP:het:22.1	0/1:TP:gm:tv:SNP:het:22.1	0|1:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	19:50474861	49971604
Common		GRCh38			19	chr19	50474861	49971604	9	FN	C	G	GT:BD:BK:QQ:BI:BVT:BLT	0|1:TP:gm:100:tv:SNP:het	0/1:TP:gm:100:tv:SNP:het	CommonFN			yes	no	Dense region of variants on one haplotype in SIGLEC16, possibly related to past gene conversions with nearby SIGLEC11, which causes short reads to miss one haplotype													0|1:TP:gm:703.77:tv:SNP:het	0/1:TP:gm:703.77:tv:SNP:het	0|1:FN:.:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:.:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:TP:gm:18.7:tv:SNP:het	0/1:TP:gm:18.7:tv:SNP:het	0|1:FN:.:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:.:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:.:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall		50474861
Common		GRCh37			19	chr19	50474870	49971613	0	FN	G	A	GT:BD:BK:BI:BVT:BLT:QQ	0|1:TP:gm:ti:SNP:het:100	0/1:TP:gm:ti:SNP:het:100	CommonFN			yes	no	Dense region of variants on one haplotype in SIGLEC16, possibly related to past gene conversions with nearby SIGLEC11, which causes short reads to miss one haplotype													0|1:TP:gm:ti:SNP:het:703.77	0/1:TP:gm:ti:SNP:het:703.77	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:TP:gm:ti:SNP:het:34.1	0/1:TP:gm:ti:SNP:het:34.1	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	19:50474870	49971613
Common		GRCh38			19	chr19	50474870	49971613	13	FN	G	A	GT:BD:BK:QQ:BI:BVT:BLT	0|1:TP:gm:100:ti:SNP:het	0/1:TP:gm:100:ti:SNP:het	CommonFN			yes	no	Dense region of variants on one haplotype in SIGLEC16, possibly related to past gene conversions with nearby SIGLEC11, which causes short reads to miss one haplotype													0|1:TP:gm:703.77:ti:SNP:het	0/1:TP:gm:703.77:ti:SNP:het	0|1:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:TP:gm:33.7:ti:SNP:het	0/1:TP:gm:33.7:ti:SNP:het	0|1:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall		50474870
Common		GRCh37			19	chr19	50474883	49971626	0	FN	T	C	GT:BD:BK:BI:BVT:BLT:QQ	0|1:TP:gm:ti:SNP:het:100	0/1:TP:gm:ti:SNP:het:100	CommonFN			yes	no	Dense region of variants on one haplotype in SIGLEC16, possibly related to past gene conversions with nearby SIGLEC11, which causes short reads to miss one haplotype													0|1:TP:gm:ti:SNP:het:703.77	0/1:TP:gm:ti:SNP:het:703.77	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:TP:gm:ti:SNP:het:26.7	0/1:TP:gm:ti:SNP:het:26.7	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	19:50474883	49971626
Common		GRCh38			19	chr19	50474883	49971626	9	FN	T	C	GT:BD:BK:QQ:BI:BVT:BLT	0|1:TP:gm:100:ti:SNP:het	0/1:TP:gm:100:ti:SNP:het	CommonFN			yes	no	Dense region of variants on one haplotype in SIGLEC16, possibly related to past gene conversions with nearby SIGLEC11, which causes short reads to miss one haplotype													0|1:TP:gm:703.77:ti:SNP:het	0/1:TP:gm:703.77:ti:SNP:het	0|1:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:TP:gm:35.6:ti:SNP:het	0/1:TP:gm:35.6:ti:SNP:het	0|1:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall		50474883
Common		GRCh37			19	chr19	50474892	49971635	0	FN	C	T	GT:BD:BK:BI:BVT:BLT:QQ	0|1:TP:gm:ti:SNP:het:100	0/1:TP:gm:ti:SNP:het:100	CommonFN			yes	no	Dense region of variants on one haplotype in SIGLEC16, possibly related to past gene conversions with nearby SIGLEC11, which causes short reads to miss one haplotype													0|1:TP:gm:ti:SNP:het:703.77	0/1:TP:gm:ti:SNP:het:703.77	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:TP:gm:ti:SNP:het:38.2	0/1:TP:gm:ti:SNP:het:38.2	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	19:50474892	49971635
Common		GRCh38			19	chr19	50474892	49971635	125	FN	C	T	GT:BD:BK:QQ:BI:BVT:BLT	0|1:TP:gm:100:ti:SNP:het	0/1:TP:gm:100:ti:SNP:het	CommonFN			yes	no	Dense region of variants on one haplotype in SIGLEC16, possibly related to past gene conversions with nearby SIGLEC11, which causes short reads to miss one haplotype													0|1:TP:gm:703.77:ti:SNP:het	0/1:TP:gm:703.77:ti:SNP:het	0|1:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:TP:gm:43:ti:SNP:het	0/1:TP:gm:43:ti:SNP:het	0|1:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall		50474892
Common		GRCh37			19	chr19	50475017	49971760	0	FP_FN	G	A	GT:BD:BK:QQ:BI:BVT:BLT	1|0:TP:gm:100:ti:SNP:het	0/1:TP:gm:100:ti:SNP:het	CommonFP_FN			yes	no	Dense region of variants on one haplotype in SIGLEC16, possibly related to past gene conversions with nearby SIGLEC11, which causes short reads to miss one haplotype													1|0:TP:gm:796.77:ti:SNP:het	0/1:TP:gm:796.77:ti:SNP:het	1|0:FN:am:.:ti:SNP:het	1/1:FP:am:1052.77:ti:SNP:homalt	1|0:FN:am:.:ti:SNP:het	1/1:FP:am:30:ti:SNP:homalt	1|0:TP:gm:307.63:ti:SNP:het	0/1:TP:gm:307.63:ti:SNP:het	1|0:FN:am:.:ti:SNP:het	1/1:FP:am:0:ti:SNP:homalt	1|0:FN:am:.:ti:SNP:het	1/1:FP:am:86.44:ti:SNP:homalt	1|0:FN:am:.:ti:SNP:het	1/1:FP:am:36:ti:SNP:homalt	19:50475017	49971760
Common		GRCh38			19	chr19	50475017	49971760	10	FP_FN	G	A	GT:BD:BK:QQ:BI:BVT:BLT	1|0:TP:gm:100:ti:SNP:het	0/1:TP:gm:100:ti:SNP:het	CommonFP_FN			yes	no	Dense region of variants on one haplotype in SIGLEC16, possibly related to past gene conversions with nearby SIGLEC11, which causes short reads to miss one haplotype													1|0:TP:gm:796.77:ti:SNP:het	0/1:TP:gm:796.77:ti:SNP:het	1|0:FN:am:.:ti:SNP:het	1/1:FP:am:1013.77:ti:SNP:homalt	1|0:FN:am:.:ti:SNP:het	1/1:FP:am:30:ti:SNP:homalt	1|0:FN:am:.:ti:SNP:het	1/1:FP:am:535.99:ti:SNP:homalt	1|0:FN:am:.:ti:SNP:het	1/1:FP:am:0:ti:SNP:homalt	1|0:FN:am:.:ti:SNP:het	1/1:FP:am:86.44:ti:SNP:homalt	1|0:FN:am:.:ti:SNP:het	1/1:FP:am:36:ti:SNP:homalt		50475017
Common		GRCh37			19	chr19	50475027	49971770	0	FN	T	A	GT:BD:BK:BI:BVT:BLT:QQ	0|1:TP:gm:tv:SNP:het:100	0/1:TP:gm:tv:SNP:het:100	CommonFN			yes	no	Dense region of variants on one haplotype in SIGLEC16, possibly related to past gene conversions with nearby SIGLEC11, which causes short reads to miss one haplotype													0|1:TP:gm:tv:SNP:het:706.77	0/1:TP:gm:tv:SNP:het:706.77	0|1:FN:lm:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:TP:gm:tv:SNP:het:56.3	0/1:TP:gm:tv:SNP:het:56.3	0|1:FN:lm:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	19:50475027	49971770
Common		GRCh38			19	chr19	50475027	49971770	17	FN	T	A	GT:BD:BK:QQ:BI:BVT:BLT	0|1:TP:gm:100:tv:SNP:het	0/1:TP:gm:100:tv:SNP:het	CommonFN			yes	no	Dense region of variants on one haplotype in SIGLEC16, possibly related to past gene conversions with nearby SIGLEC11, which causes short reads to miss one haplotype													0|1:TP:gm:706.77:tv:SNP:het	0/1:TP:gm:706.77:tv:SNP:het	0|1:FN:lm:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:lm:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:TP:gm:49.8:tv:SNP:het	0/1:TP:gm:49.8:tv:SNP:het	0|1:FN:lm:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:lm:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:lm:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall		50475027
Common		GRCh37			19	chr19	50475044	49971787	0	FN	T	C	GT:BD:BK:BI:BVT:BLT:QQ	0|1:TP:gm:ti:SNP:het:100	0/1:TP:gm:ti:SNP:het:100	CommonFN			yes	no	Dense region of variants on one haplotype in SIGLEC16, possibly related to past gene conversions with nearby SIGLEC11, which causes short reads to miss one haplotype													0|1:TP:gm:ti:SNP:het:706.77	0/1:TP:gm:ti:SNP:het:706.77	0|1:FN:lm:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	19:50475044	49971787
Common		GRCh38			19	chr19	50475044	49971787	1	FN	T	C	GT:BD:BK:QQ:BI:BVT:BLT	0|1:TP:gm:100:ti:SNP:het	0/1:TP:gm:100:ti:SNP:het	CommonFN			yes	no	Dense region of variants on one haplotype in SIGLEC16, possibly related to past gene conversions with nearby SIGLEC11, which causes short reads to miss one haplotype													0|1:TP:gm:706.77:ti:SNP:het	0/1:TP:gm:706.77:ti:SNP:het	0|1:FN:lm:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:lm:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:lm:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:lm:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:lm:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:lm:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall		50475044
ITER	ITERteam_small-variation_GRCh37_ILMN-PB-ONT.vcf.gz	GRCh37	small-variants	SNP	19	chr19	50475045	49971788	0	FN	G	A	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:lm:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	Yes	No		yes	no	Dense region of variants on one haplotype in SIGLEC16, possibly related to past gene conversions with nearby SIGLEC11, which causes short reads to miss one haplotype																											19:50475045	49971788
Common		GRCh37			19	chr19	50475045	49971788	0	FN	G	A	GT:BD:BK:BI:BVT:BLT:QQ	0|1:TP:gm:ti:SNP:het:36.989	0/1:TP:gm:ti:SNP:het:36.989	CommonFN			yes	no	Dense region of variants on one haplotype in SIGLEC16, possibly related to past gene conversions with nearby SIGLEC11, which causes short reads to miss one haplotype													0|1:TP:gm:ti:SNP:het:706.77	0/1:TP:gm:ti:SNP:het:706.77	0|1:FN:lm:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	19:50475045	49971788
Common		GRCh38			19	chr19	50475045	49971788	5	FN	G	A	GT:BD:BK:QQ:BI:BVT:BLT	0|1:TP:gm:100:ti:SNP:het	0/1:TP:gm:100:ti:SNP:het	CommonFN			yes	no	Dense region of variants on one haplotype in SIGLEC16, possibly related to past gene conversions with nearby SIGLEC11, which causes short reads to miss one haplotype													0|1:TP:gm:706.77:ti:SNP:het	0/1:TP:gm:706.77:ti:SNP:het	0|1:FN:lm:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:lm:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:lm:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:lm:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:lm:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:lm:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall		50475045
Common		GRCh37			19	chr19	50475050	49971793	0	FN	C	A	GT:BD:BK:BI:BVT:BLT:QQ	0|1:TP:gm:tv:SNP:het:29.5872	0/1:TP:gm:tv:SNP:het:29.5872	CommonFN			yes	no	Dense region of variants on one haplotype in SIGLEC16, possibly related to past gene conversions with nearby SIGLEC11, which causes short reads to miss one haplotype													0|1:TP:gm:tv:SNP:het:706.77	0/1:TP:gm:tv:SNP:het:706.77	0|1:FN:lm:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:TP:gm:tv:SNP:het:39.9	0/1:TP:gm:tv:SNP:het:39.9	0|1:FN:lm:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	19:50475050	49971793
Common		GRCh38			19	chr19	50475050	49971793	25	FN	C	A	GT:BD:BK:QQ:BI:BVT:BLT	0|1:TP:gm:29.5872:tv:SNP:het	0/1:TP:gm:29.5872:tv:SNP:het	CommonFN			yes	no	Dense region of variants on one haplotype in SIGLEC16, possibly related to past gene conversions with nearby SIGLEC11, which causes short reads to miss one haplotype													0|1:TP:gm:706.77:tv:SNP:het	0/1:TP:gm:706.77:tv:SNP:het	0|1:FN:lm:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:lm:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:TP:gm:31:tv:SNP:het	0/1:TP:gm:31:tv:SNP:het	0|1:FN:lm:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:lm:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:lm:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall		50475050
Common		GRCh37			19	chr19	50475075	49971818	0	FP_FN	G	A	GT:BD:BK:QQ:BI:BVT:BLT	1|0:TP:gm:100:ti:SNP:het	0/1:TP:gm:100:ti:SNP:het	CommonFP_FN			yes	no	Dense region of variants on one haplotype in SIGLEC16, possibly related to past gene conversions with nearby SIGLEC11, which causes short reads to miss one haplotype													1|0:TP:gm:796.77:ti:SNP:het	0/1:TP:gm:796.77:ti:SNP:het	1|0:FN:am:.:ti:SNP:het	1/1:FP:am:1321.77:ti:SNP:homalt	1|0:FN:am:.:ti:SNP:het	1/1:FP:am:30:ti:SNP:homalt	1|0:FN:am:.:ti:SNP:het	1/1:FP:am:661.03:ti:SNP:homalt	1|0:FN:am:.:ti:SNP:het	1/1:FP:am:0:ti:SNP:homalt	1|0:FN:am:.:ti:SNP:het	1/1:FP:am:83.43:ti:SNP:homalt	1|0:FN:am:.:ti:SNP:het	1/1:FP:am:36:ti:SNP:homalt	19:50475075	49971818
Common		GRCh38			19	chr19	50475075	49971818	1	FP_FN	G	A	GT:BD:BK:QQ:BI:BVT:BLT	1|0:TP:gm:36.989:ti:SNP:het	0/1:TP:gm:36.989:ti:SNP:het	CommonFP_FN			yes	no	Dense region of variants on one haplotype in SIGLEC16, possibly related to past gene conversions with nearby SIGLEC11, which causes short reads to miss one haplotype													1|0:TP:gm:796.77:ti:SNP:het	0/1:TP:gm:796.77:ti:SNP:het	1|0:FN:am:.:ti:SNP:het	1/1:FP:am:1276.77:ti:SNP:homalt	1|0:FN:am:.:ti:SNP:het	1/1:FP:am:30:ti:SNP:homalt	1|0:FN:am:.:ti:SNP:het	1/1:FP:am:898.03:ti:SNP:homalt	1|0:FN:am:.:ti:SNP:het	1/1:FP:am:0:ti:SNP:homalt	1|0:FN:am:.:ti:SNP:het	1/1:FP:am:83.43:ti:SNP:homalt	1|0:FN:am:.:ti:SNP:het	1/1:FP:am:36:ti:SNP:homalt		50475075
BCM-HGSC_xAtlas	HG002.hs37d5.60x.1_merged.vcf.gz	GRCh37	small-variants	SNP	19	chr19	50475076	49971819	0	FP_FN	T	A	GT:BD:BK:QQ:BI:BVT:BLT	1|0:FN:am:.:tv:SNP:het	1/1:FP:am:35:tv:SNP:homalt 	Yes	No		yes	no	Dense region of variants on one haplotype in SIGLEC16, possibly related to past gene conversions with nearby SIGLEC11, which causes short reads to miss one haplotype																											19:50475076	49971819
ITER	ITERteam_small-variation_GRCh37_ILMN-PB-ONT.vcf.gz	GRCh37	small-variants	SNP	19	chr19	50475076	49971819	0	FP_FN	T	A	GT:BD:BK:QQ:BI:BVT:BLT	1|0:FN:am:.:tv:SNP:het	1/1:FP:am:661.03:tv:SNP:homalt	Unsure	Unsure	Short reads support homalt genotype and long reads support het genotype.	yes	no	Dense region of variants on one haplotype in SIGLEC16, possibly related to past gene conversions with nearby SIGLEC11, which causes short reads to miss one haplotype																											19:50475076	49971819
Common		GRCh37			19	chr19	50475076	49971819	0	FP_FN	T	A	GT:BD:BK:QQ:BI:BVT:BLT	1|0:TP:gm:100:tv:SNP:het	0/1:TP:gm:100:tv:SNP:het	CommonFP_FN			yes	no	Dense region of variants on one haplotype in SIGLEC16, possibly related to past gene conversions with nearby SIGLEC11, which causes short reads to miss one haplotype													1|0:TP:gm:796.77:tv:SNP:het	0/1:TP:gm:796.77:tv:SNP:het	1|0:FN:am:.:tv:SNP:het	1/1:FP:am:1321.77:tv:SNP:homalt	1|0:FN:am:.:tv:SNP:het	1/1:FP:am:30:tv:SNP:homalt	1|0:FN:am:.:tv:SNP:het	1/1:FP:am:661.03:tv:SNP:homalt	1|0:FN:am:.:tv:SNP:het	1/1:FP:am:0:tv:SNP:homalt	1|0:FN:am:.:tv:SNP:het	1/1:FP:am:83.43:tv:SNP:homalt	1|0:FN:am:.:tv:SNP:het	1/1:FP:am:35:tv:SNP:homalt	19:50475076	49971819
Common		GRCh38			19	chr19	50475076	49971819	1	FP_FN	T	A	GT:BD:BK:QQ:BI:BVT:BLT	1|0:TP:gm:100:tv:SNP:het	0/1:TP:gm:100:tv:SNP:het	CommonFP_FN			yes	no	Dense region of variants on one haplotype in SIGLEC16, possibly related to past gene conversions with nearby SIGLEC11, which causes short reads to miss one haplotype													1|0:TP:gm:796.77:tv:SNP:het	0/1:TP:gm:796.77:tv:SNP:het	1|0:FN:am:.:tv:SNP:het	1/1:FP:am:1276.77:tv:SNP:homalt	1|0:FN:am:.:tv:SNP:het	1/1:FP:am:30:tv:SNP:homalt	1|0:FN:am:.:tv:SNP:het	1/1:FP:am:898.03:tv:SNP:homalt	1|0:FN:am:.:tv:SNP:het	1/1:FP:am:0:tv:SNP:homalt	1|0:FN:am:.:tv:SNP:het	1/1:FP:am:83.43:tv:SNP:homalt	1|0:FN:am:.:tv:SNP:het	1/1:FP:am:35:tv:SNP:homalt		50475076
Common		GRCh37			19	chr19	50475077	49971820	0	FP_FN	C	T	GT:BD:BK:QQ:BI:BVT:BLT	1|0:TP:gm:19.0792:ti:SNP:het	0/1:TP:gm:19.0792:ti:SNP:het	CommonFP_FN			yes	no	Dense region of variants on one haplotype in SIGLEC16, possibly related to past gene conversions with nearby SIGLEC11, which causes short reads to miss one haplotype													1|0:TP:gm:796.77:ti:SNP:het	0/1:TP:gm:796.77:ti:SNP:het	1|0:FN:am:.:ti:SNP:het	1/1:FP:am:1321.77:ti:SNP:homalt	1|0:FN:am:.:ti:SNP:het	1/1:FP:am:30:ti:SNP:homalt	1|0:FN:am:.:ti:SNP:het	1/1:FP:am:661.03:ti:SNP:homalt	1|0:FN:am:.:ti:SNP:het	1/1:FP:am:0:ti:SNP:homalt	1|0:FN:am:.:ti:SNP:het	1/1:FP:am:83.43:ti:SNP:homalt	1|0:FN:am:.:ti:SNP:het	1/1:FP:am:36:ti:SNP:homalt	19:50475077	49971820
Common		GRCh38			19	chr19	50475077	49971820	38	FP_FN	C	T	GT:BD:BK:QQ:BI:BVT:BLT	1|0:TP:gm:20.7663:ti:SNP:het	0/1:TP:gm:20.7663:ti:SNP:het	CommonFP_FN			yes	no	Dense region of variants on one haplotype in SIGLEC16, possibly related to past gene conversions with nearby SIGLEC11, which causes short reads to miss one haplotype													1|0:TP:gm:796.77:ti:SNP:het	0/1:TP:gm:796.77:ti:SNP:het	1|0:FN:am:.:ti:SNP:het	1/1:FP:am:1276.77:ti:SNP:homalt	1|0:FN:am:.:ti:SNP:het	1/1:FP:am:30:ti:SNP:homalt	1|0:FN:am:.:ti:SNP:het	1/1:FP:am:898.03:ti:SNP:homalt	1|0:FN:am:.:ti:SNP:het	1/1:FP:am:0:ti:SNP:homalt	1|0:FN:am:.:ti:SNP:het	1/1:FP:am:83.43:ti:SNP:homalt	1|0:FN:am:.:ti:SNP:het	1/1:FP:am:36:ti:SNP:homalt		50475077
ITER	ITERteam_small-variation_GRCh37_ILMN-PB-ONT.vcf.gz	GRCh37	small-variants	SNP	19	chr19	50475115	49971858	0	FN	A	G	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:lm:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	Unsure	Unsure	Variant only supported by PacBio. The variant in previous position is detected by all technologies in both truth and query.	yes	no	Dense region of variants on one haplotype in SIGLEC16, possibly related to past gene conversions with nearby SIGLEC11, which causes short reads to miss one haplotype																											19:50475115	49971858
Common		GRCh37			19	chr19	50475115	49971858	0	FN	A	G	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:lm:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	Dense region of variants on one haplotype in SIGLEC16, possibly related to past gene conversions with nearby SIGLEC11, which causes short reads to miss one haplotype													0|1:TP:gm:ti:SNP:het:607.77	0/1:TP:gm:ti:SNP:het:607.77	0|1:FN:lm:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	19:50475115	49971858
Common		GRCh38			19	chr19	50475115	49971858	19	FN	A	G	GT:BD:BK:QQ:BI:BVT:BLT	0|1:TP:gm:19.1476:ti:SNP:het	0/1:TP:gm:19.1476:ti:SNP:het	CommonFN			yes	no	Dense region of variants on one haplotype in SIGLEC16, possibly related to past gene conversions with nearby SIGLEC11, which causes short reads to miss one haplotype													0|1:TP:gm:607.77:ti:SNP:het	0/1:TP:gm:607.77:ti:SNP:het	0|1:FN:lm:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:lm:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:lm:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:lm:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:lm:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:lm:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall		50475115
Common		GRCh37			19	chr19	50475134	49971877	0	FN	G	C	GT:BD:BK:BI:BVT:BLT:QQ	0|1:TP:gm:tv:SNP:het:36.989	0/1:TP:gm:tv:SNP:het:36.989	CommonFN			yes	no	Dense region of variants on one haplotype in SIGLEC16, possibly related to past gene conversions with nearby SIGLEC11, which causes short reads to miss one haplotype													0|1:TP:gm:tv:SNP:het:706.77	0/1:TP:gm:tv:SNP:het:706.77	0|1:FN:lm:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:TP:gm:tv:SNP:het:50.1	0/1:TP:gm:tv:SNP:het:50.1	0|1:FN:lm:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	19:50475134	49971877
NCBI	HG002_grch38_dipcall.vcf.gz	GRCh38	small-variants	SNP	19	chr19	50475134	49971877	0	FN	G	C	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:lm:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	yes	no	segdup region; only PB/ONT support benchmark	yes	no	Dense region of variants on one haplotype in SIGLEC16, possibly related to past gene conversions with nearby SIGLEC11, which causes short reads to miss one haplotype				skip																								50475134
Common		GRCh38			19	chr19	50475134	49971877	25	FN	G	C	GT:BD:BK:QQ:BI:BVT:BLT	0|1:TP:gm:100:tv:SNP:het	0/1:TP:gm:100:tv:SNP:het	CommonFN			yes	no	Dense region of variants on one haplotype in SIGLEC16, possibly related to past gene conversions with nearby SIGLEC11, which causes short reads to miss one haplotype													0|1:TP:gm:706.77:tv:SNP:het	0/1:TP:gm:706.77:tv:SNP:het	0|1:FN:lm:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:lm:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:TP:gm:53.3:tv:SNP:het	0/1:TP:gm:53.3:tv:SNP:het	0|1:FN:lm:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:lm:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:lm:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall		50475134
Common		GRCh37			19	chr19	50475159	49971902	0	FN	T	C	GT:BD:BK:BI:BVT:BLT:QQ	0|1:TP:gm:ti:SNP:het:23.7716	0/1:TP:gm:ti:SNP:het:23.7716	CommonFN			yes	no	Dense region of variants on one haplotype in SIGLEC16, possibly related to past gene conversions with nearby SIGLEC11, which causes short reads to miss one haplotype													0|1:TP:gm:ti:SNP:het:625.77	0/1:TP:gm:ti:SNP:het:625.77	0|1:FN:lm:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:TP:gm:ti:SNP:het:44.8	0/1:TP:gm:ti:SNP:het:44.8	0|1:FN:lm:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	19:50475159	49971902
Common		GRCh38			19	chr19	50475159	49971902	49	FN	T	C	GT:BD:BK:QQ:BI:BVT:BLT	0|1:TP:gm:100:ti:SNP:het	0/1:TP:gm:100:ti:SNP:het	CommonFN			yes	no	Dense region of variants on one haplotype in SIGLEC16, possibly related to past gene conversions with nearby SIGLEC11, which causes short reads to miss one haplotype													0|1:TP:gm:625.77:ti:SNP:het	0/1:TP:gm:625.77:ti:SNP:het	0|1:FN:lm:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:lm:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:TP:gm:49:ti:SNP:het	0/1:TP:gm:49:ti:SNP:het	0|1:FN:lm:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:lm:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:lm:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall		50475159
CMH_DRAGEN_3.6.3	NA24385.hard-filtered.vcf.gz	GRCh37	small-variants	SNP	19	chr19	50475208	49971951	0	FP_FN	C	T	GT:BD:BK:QQ:BI:BVT:BLT	1|0:FN:am:.:ti:SNP:het	1/1:FP:am:105.03:ti:SNP:homalt	yes	no		yes	no	Dense region of variants on one haplotype in SIGLEC16, possibly related to past gene conversions with nearby SIGLEC11, which causes short reads to miss one haplotype																											19:50475208	49971951
ITER	ITERteam_small-variation_GRCh37_ILMN-PB-ONT.vcf.gz	GRCh37	small-variants	SNP	19	chr19	50475208	49971951	0	FP_FN	C	T	GT:BD:BK:QQ:BI:BVT:BLT	1|0:FN:am:.:ti:SNP:het	1/1:FP:am:1066.03:ti:SNP:homalt	Unsure	Unsure	Short reads support homalt genotype and long reads support het genotype.	yes	no	Dense region of variants on one haplotype in SIGLEC16, possibly related to past gene conversions with nearby SIGLEC11, which causes short reads to miss one haplotype																											19:50475208	49971951
Common		GRCh37			19	chr19	50475208	49971951	0	FP_FN	C	T	GT:BD:BK:QQ:BI:BVT:BLT	1|0:FN:am:.:ti:SNP:het	1/1:FP:am:100:ti:SNP:homalt	CommonFP_FN			yes	no	Dense region of variants on one haplotype in SIGLEC16, possibly related to past gene conversions with nearby SIGLEC11, which causes short reads to miss one haplotype													1|0:TP:gm:760.77:ti:SNP:het	0/1:TP:gm:760.77:ti:SNP:het	1|0:FN:am:.:ti:SNP:het	1/1:FP:am:812.77:ti:SNP:homalt	1|0:FN:am:.:ti:SNP:het	1/1:FP:am:30:ti:SNP:homalt	1|0:FN:am:.:ti:SNP:het	1/1:FP:am:1066.03:ti:SNP:homalt	1|0:FN:am:.:ti:SNP:het	1/1:FP:am:0:ti:SNP:homalt	1|0:FN:am:.:ti:SNP:het	1/1:FP:am:105.03:ti:SNP:homalt	1|0:FN:am:.:ti:SNP:het	1/1:FP:am:35:ti:SNP:homalt	19:50475208	49971951
CMH_DRAGEN_3.6.3	NA24385.hard-filtered.vcf.gz	GRCh38	small-variants	SNP	19	chr19	50475208	49971951	0	FP_FN	C	T	GT:BD:BK:QQ:BI:BVT:BLT	1|0:FN:am:.:ti:SNP:het	1/1:FP:am:105.04:ti:SNP:homalt	yes	no		yes	no	Dense region of variants on one haplotype in SIGLEC16, possibly related to past gene conversions with nearby SIGLEC11, which causes short reads to miss one haplotype				skip																								50475208
Roche	RN_HG002_Illumina_PacBio_Oxford.vcf.gz	GRCh38	small-variants	SNP	19	chr19	50475208	49971951	0	FP_FN	C	T	GT:BD:BK:QQ:BI:BVT:BLT	1|0:FN:am:.:ti:SNP:het	1/1:FP:am:100:ti:SNP:homalt 	yes	no		yes	no	Dense region of variants on one haplotype in SIGLEC16, possibly related to past gene conversions with nearby SIGLEC11, which causes short reads to miss one haplotype				skip																								50475208
Common		GRCh38			19	chr19	50475208	49971951	3	FP_FN	C	T	GT:BD:BK:QQ:BI:BVT:BLT	1|0:FN:am:.:ti:SNP:het	1/1:FP:am:100:ti:SNP:homalt	CommonFP_FN			yes	no	Dense region of variants on one haplotype in SIGLEC16, possibly related to past gene conversions with nearby SIGLEC11, which causes short reads to miss one haplotype													1|0:TP:gm:760.77:ti:SNP:het	0/1:TP:gm:760.77:ti:SNP:het	1|0:FN:am:.:ti:SNP:het	1/1:FP:am:770.77:ti:SNP:homalt	1|0:FN:am:.:ti:SNP:het	1/1:FP:am:30:ti:SNP:homalt	1|0:FN:am:.:ti:SNP:het	1/1:FP:am:1246.03:ti:SNP:homalt	1|0:FN:am:.:ti:SNP:het	1/1:FP:am:0:ti:SNP:homalt	1|0:FN:am:.:ti:SNP:het	1/1:FP:am:105.04:ti:SNP:homalt	1|0:FN:am:.:ti:SNP:het	1/1:FP:am:35:ti:SNP:homalt		50475208
Common		GRCh37			19	chr19	50475211	49971954	0	FP_FN	T	G	GT:BD:BK:QQ:BI:BVT:BLT	1|0:FN:am:.:tv:SNP:het	1/1:FP:am:100:tv:SNP:homalt	CommonFP_FN			yes	no	Dense region of variants on one haplotype in SIGLEC16, possibly related to past gene conversions with nearby SIGLEC11, which causes short reads to miss one haplotype													1|0:TP:gm:760.77:tv:SNP:het	0/1:TP:gm:760.77:tv:SNP:het	1|0:FN:am:.:tv:SNP:het	1/1:FP:am:781.77:tv:SNP:homalt	1|0:FN:am:.:tv:SNP:het	1/1:FP:am:30:tv:SNP:homalt	1|0:FN:am:.:tv:SNP:het	1/1:FP:am:1066.03:tv:SNP:homalt	1|0:FN:am:.:tv:SNP:het	1/1:FP:am:0:tv:SNP:homalt	1|0:FN:am:.:tv:SNP:het	1/1:FP:am:105.49:tv:SNP:homalt	1|0:FN:am:.:tv:SNP:het	1/1:FP:am:35:tv:SNP:homalt	19:50475211	49971954
Common		GRCh38			19	chr19	50475211	49971954	4	FP_FN	T	G	GT:BD:BK:QQ:BI:BVT:BLT	1|0:FN:am:.:tv:SNP:het	1/1:FP:am:100:tv:SNP:homalt	CommonFP_FN			yes	no	Dense region of variants on one haplotype in SIGLEC16, possibly related to past gene conversions with nearby SIGLEC11, which causes short reads to miss one haplotype													1|0:TP:gm:760.77:tv:SNP:het	0/1:TP:gm:760.77:tv:SNP:het	1|0:FN:am:.:tv:SNP:het	1/1:FP:am:736.77:tv:SNP:homalt	1|0:FN:am:.:tv:SNP:het	1/1:FP:am:30:tv:SNP:homalt	1|0:FN:am:.:tv:SNP:het	1/1:FP:am:1246.03:tv:SNP:homalt	1|0:FN:am:.:tv:SNP:het	1/1:FP:am:0:tv:SNP:homalt	1|0:FN:am:.:tv:SNP:het	1/1:FP:am:105.49:tv:SNP:homalt	1|0:FN:am:.:tv:SNP:het	1/1:FP:am:35:tv:SNP:homalt		50475211
Common		GRCh37			19	chr19	50475215	49971958	0	FP_FN	G	A	GT:BD:BK:QQ:BI:BVT:BLT	1|0:FN:am:.:ti:SNP:het	1/1:FP:am:100:ti:SNP:homalt	CommonFP_FN			yes	no	Dense region of variants on one haplotype in SIGLEC16, possibly related to past gene conversions with nearby SIGLEC11, which causes short reads to miss one haplotype													1|0:TP:gm:760.77:ti:SNP:het	0/1:TP:gm:760.77:ti:SNP:het	1|0:FN:am:.:ti:SNP:het	1/1:FP:am:781.77:ti:SNP:homalt	1|0:FN:am:.:ti:SNP:het	1/1:FP:am:30:ti:SNP:homalt	1|0:FN:am:.:ti:SNP:het	1/1:FP:am:1066.03:ti:SNP:homalt	1|0:FN:lm:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	1|0:FN:am:.:ti:SNP:het	1/1:FP:am:108.49:ti:SNP:homalt	1|0:FN:am:.:ti:SNP:het	1/1:FP:am:34:ti:SNP:homalt	19:50475215	49971958
CMH_DRAGEN_3.6.3	NA24385.hard-filtered.vcf.gz	GRCh38	small-variants	SNP	19	chr19	50475215	49971958	0	FP_FN	G	A	GT:BD:BK:QQ:BI:BVT:BLT	1|0:FN:am:.:ti:SNP:het	1/1:FP:am:108.5:ti:SNP:homalt	yes	no		yes	no	Dense region of variants on one haplotype in SIGLEC16, possibly related to past gene conversions with nearby SIGLEC11, which causes short reads to miss one haplotype				skip																								50475215
Common		GRCh38			19	chr19	50475215	49971958	34	FP_FN	G	A	GT:BD:BK:QQ:BI:BVT:BLT	1|0:FN:am:.:ti:SNP:het	1/1:FP:am:100:ti:SNP:homalt	CommonFP_FN			yes	no	Dense region of variants on one haplotype in SIGLEC16, possibly related to past gene conversions with nearby SIGLEC11, which causes short reads to miss one haplotype													1|0:TP:gm:760.77:ti:SNP:het	0/1:TP:gm:760.77:ti:SNP:het	1|0:FN:am:.:ti:SNP:het	1/1:FP:am:736.77:ti:SNP:homalt	1|0:FN:am:.:ti:SNP:het	1/1:FP:am:30:ti:SNP:homalt	1|0:FN:am:.:ti:SNP:het	1/1:FP:am:1246.03:ti:SNP:homalt	1|0:FN:lm:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	1|0:FN:am:.:ti:SNP:het	1/1:FP:am:108.5:ti:SNP:homalt	1|0:FN:am:.:ti:SNP:het	1/1:FP:am:34:ti:SNP:homalt		50475215
Common		GRCh37			19	chr19	50475249	49971992	0	FN	T	C	GT:BD:BK:BI:BVT:BLT:QQ	0|1:TP:gm:ti:SNP:het:100	0/1:TP:gm:ti:SNP:het:100	CommonFN			yes	no	Dense region of variants on one haplotype in SIGLEC16, possibly related to past gene conversions with nearby SIGLEC11, which causes short reads to miss one haplotype													0|1:TP:gm:ti:SNP:het:625.77	0/1:TP:gm:ti:SNP:het:625.77	0|1:FN:lm:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:TP:gm:ti:SNP:het:11	0/1:TP:gm:ti:SNP:het:11	0|1:FN:lm:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	19:50475249	49971992
Common		GRCh38			19	chr19	50475249	49971992	10	FN	T	C	GT:BD:BK:QQ:BI:BVT:BLT	0|1:TP:gm:100:ti:SNP:het	0/1:TP:gm:100:ti:SNP:het	CommonFN			yes	no	Dense region of variants on one haplotype in SIGLEC16, possibly related to past gene conversions with nearby SIGLEC11, which causes short reads to miss one haplotype													0|1:TP:gm:625.77:ti:SNP:het	0/1:TP:gm:625.77:ti:SNP:het	0|1:FN:lm:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:lm:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:TP:gm:21.9:ti:SNP:het	0/1:TP:gm:21.9:ti:SNP:het	0|1:FN:lm:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:lm:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:lm:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall		50475249
BCM-HGSC_xAtlas	HG002.hs37d5.60x.1_merged.vcf.gz	GRCh37	small-variants	SNP	19	chr19	50475259	49972002	0	FP_FN	G	C	GT:BD:BK:QQ:BI:BVT:BLT	1|0:FN:am:.:tv:SNP:het	1/1:FP:am:34:tv:SNP:homalt 	Yes	No		yes	no	Dense region of variants on one haplotype in SIGLEC16, possibly related to past gene conversions with nearby SIGLEC11, which causes short reads to miss one haplotype																											19:50475259	49972002
Common		GRCh37			19	chr19	50475259	49972002	0	FP_FN	G	C	GT:BD:BK:QQ:BI:BVT:BLT	1|0:TP:gm:30.0008:tv:SNP:het	0/1:TP:gm:30.0008:tv:SNP:het	CommonFP_FN			yes	no	Dense region of variants on one haplotype in SIGLEC16, possibly related to past gene conversions with nearby SIGLEC11, which causes short reads to miss one haplotype													1|0:TP:gm:760.77:tv:SNP:het	0/1:TP:gm:760.77:tv:SNP:het	1|0:FN:am:.:tv:SNP:het	1/1:FP:am:535.77:tv:SNP:homalt	1|0:FN:am:.:tv:SNP:het	1/1:FP:am:30:tv:SNP:homalt	1|0:FN:am:.:tv:SNP:het	1/1:FP:am:845.03:tv:SNP:homalt	1|0:FN:am:.:tv:SNP:het	1/1:FP:am:0:tv:SNP:homalt	1|0:FN:am:.:tv:SNP:het	1/1:FP:am:102.94:tv:SNP:homalt	1|0:FN:am:.:tv:SNP:het	1/1:FP:am:34:tv:SNP:homalt	19:50475259	49972002
Common		GRCh38			19	chr19	50475259	49972002	8	FP_FN	G	C	GT:BD:BK:QQ:BI:BVT:BLT	1|0:TP:gm:30.0008:tv:SNP:het	0/1:TP:gm:30.0008:tv:SNP:het	CommonFP_FN			yes	no	Dense region of variants on one haplotype in SIGLEC16, possibly related to past gene conversions with nearby SIGLEC11, which causes short reads to miss one haplotype													1|0:TP:gm:760.77:tv:SNP:het	0/1:TP:gm:760.77:tv:SNP:het	1|0:FN:am:.:tv:SNP:het	1/1:FP:am:502.77:tv:SNP:homalt	1|0:FN:am:.:tv:SNP:het	1/1:FP:am:30:tv:SNP:homalt	1|0:FN:am:.:tv:SNP:het	1/1:FP:am:571.03:tv:SNP:homalt	1|0:FN:am:.:tv:SNP:het	1/1:FP:am:0:tv:SNP:homalt	1|0:FN:am:.:tv:SNP:het	1/1:FP:am:102.94:tv:SNP:homalt	1|0:FN:am:.:tv:SNP:het	1/1:FP:am:34:tv:SNP:homalt		50475259
Common		GRCh37			19	chr19	50475267	49972010	0	FN	T	A	GT:BD:BK:BI:BVT:BLT:QQ	0|1:TP:gm:tv:SNP:het:100	0/1:TP:gm:tv:SNP:het:100	CommonFN			yes	no	Dense region of variants on one haplotype in SIGLEC16, possibly related to past gene conversions with nearby SIGLEC11, which causes short reads to miss one haplotype													0|1:TP:gm:tv:SNP:het:625.77	0/1:TP:gm:tv:SNP:het:625.77	0|1:FN:lm:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:TP:gm:tv:SNP:het:4.1	0/1:TP:gm:tv:SNP:het:4.1	0|1:FN:lm:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	19:50475267	49972010
Common		GRCh38			19	chr19	50475267	49972010	2	FN	T	A	GT:BD:BK:QQ:BI:BVT:BLT	0|1:TP:gm:100:tv:SNP:het	0/1:TP:gm:100:tv:SNP:het	CommonFN			yes	no	Dense region of variants on one haplotype in SIGLEC16, possibly related to past gene conversions with nearby SIGLEC11, which causes short reads to miss one haplotype													0|1:TP:gm:625.77:tv:SNP:het	0/1:TP:gm:625.77:tv:SNP:het	0|1:FN:lm:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:lm:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:TP:gm:4.9:tv:SNP:het	0/1:TP:gm:4.9:tv:SNP:het	0|1:FN:lm:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:lm:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:lm:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall		50475267
Common		GRCh37			19	chr19	50475269	49972012	0	FN	G	C	GT:BD:BK:BI:BVT:BLT:QQ	0|1:TP:gm:tv:SNP:het:17.6374	0/1:TP:gm:tv:SNP:het:17.6374	CommonFN			yes	no	Dense region of variants on one haplotype in SIGLEC16, possibly related to past gene conversions with nearby SIGLEC11, which causes short reads to miss one haplotype													0|1:TP:gm:tv:SNP:het:625.77	0/1:TP:gm:tv:SNP:het:625.77	0|1:FN:lm:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	19:50475269	49972012
Common		GRCh38			19	chr19	50475269	49972012	1	FN	G	C	GT:BD:BK:QQ:BI:BVT:BLT	0|1:TP:gm:100:tv:SNP:het	0/1:TP:gm:100:tv:SNP:het	CommonFN			yes	no	Dense region of variants on one haplotype in SIGLEC16, possibly related to past gene conversions with nearby SIGLEC11, which causes short reads to miss one haplotype													0|1:TP:gm:625.77:tv:SNP:het	0/1:TP:gm:625.77:tv:SNP:het	0|1:FN:lm:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:lm:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:lm:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:lm:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:lm:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:lm:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall		50475269
Common		GRCh37			19	chr19	50475270	49972013	0	FN	G	C	GT:BD:BK:BI:BVT:BLT:QQ	0|1:TP:gm:tv:SNP:het:39.9993	0/1:TP:gm:tv:SNP:het:39.9993	CommonFN			yes	no	Dense region of variants on one haplotype in SIGLEC16, possibly related to past gene conversions with nearby SIGLEC11, which causes short reads to miss one haplotype													0|1:TP:gm:tv:SNP:het:625.77	0/1:TP:gm:tv:SNP:het:625.77	0|1:FN:lm:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	19:50475270	49972013
Common		GRCh38			19	chr19	50475270	49972013	1	FN	G	C	GT:BD:BK:QQ:BI:BVT:BLT	0|1:TP:gm:100:tv:SNP:het	0/1:TP:gm:100:tv:SNP:het	CommonFN			yes	no	Dense region of variants on one haplotype in SIGLEC16, possibly related to past gene conversions with nearby SIGLEC11, which causes short reads to miss one haplotype													0|1:TP:gm:625.77:tv:SNP:het	0/1:TP:gm:625.77:tv:SNP:het	0|1:FN:lm:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:lm:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:lm:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:lm:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:lm:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:lm:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall		50475270
Common		GRCh37			19	chr19	50475271	49972014	0	FN	G	A	GT:BD:BK:BI:BVT:BLT:QQ	0|1:TP:gm:ti:SNP:het:39.9993	0/1:TP:gm:ti:SNP:het:39.9993	CommonFN			yes	no	Dense region of variants on one haplotype in SIGLEC16, possibly related to past gene conversions with nearby SIGLEC11, which causes short reads to miss one haplotype													0|1:TP:gm:ti:SNP:het:625.77	0/1:TP:gm:ti:SNP:het:625.77	0|1:FN:lm:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	19:50475271	49972014
Common		GRCh38			19	chr19	50475271	49972014	1385472	FN	G	A	GT:BD:BK:QQ:BI:BVT:BLT	0|1:TP:gm:100:ti:SNP:het	0/1:TP:gm:100:ti:SNP:het	CommonFN			yes	no	Dense region of variants on one haplotype in SIGLEC16, possibly related to past gene conversions with nearby SIGLEC11, which causes short reads to miss one haplotype													0|1:TP:gm:625.77:ti:SNP:het	0/1:TP:gm:625.77:ti:SNP:het	0|1:FN:lm:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:lm:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:lm:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:lm:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:lm:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:lm:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall		50475271
NCBI	HG002_grch37_dipcall.vcf.gz	GRCh37	small-variants	INDEL	19	chr19	51860740	51357486	2461523	FN	C	CT	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:lm:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	yes	no	repeat region																														19:51860740	51357486
Roche	RN_HG002_Illumina_PacBio_Oxford_GRCh37.vcf.gz	GRCh37	small-variants	INDEL	19	chr19	54322263	53819009	0	FN	TGG	T	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0 	no	yes	no evidence in any technology	no	yes	looks like hifiasm consensus error since no support in reads from any tech																											19:54322263	53819009
Common		GRCh37			19	chr19	54322263	53819009	0	FN	TGG	T	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no	yes	looks like hifiasm consensus error since no support in reads from any tech													0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	19:54322263	53819009
Common		GRCh38			19	chr19	54322263	53819009	77367	FN	TGG	T	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no	yes	looks like hifiasm consensus error since no support in reads from any tech													0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0		54322263
Common		GRCh37			19	chr19	54399630	53896376	0	FP_FN	GATTATTATT	G	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:d6_15:INDEL:homalt	0/1:FP:am:100:d6_15:INDEL:het	CommonFP_FN			no	yes	benchmark misses haplotype in TR likely due to highly homozygous region													1|1:FN:am:.:d6_15:INDEL:homalt	0/1:FP:am:1354.73:d6_15:INDEL:het	1|1:FN:am:.:d6_15:INDEL:homalt	0/1:FP:am:1538.73:d6_15:INDEL:het	1|1:FN:am:.:d6_15:INDEL:homalt	0/1:FP:am:30:d6_15:INDEL:het	1|1:FN:am:.:d6_15:INDEL:homalt	0/1:FP:am:1331.06:d6_15:INDEL:het	1|1:FN:am:.:d6_15:INDEL:homalt	0/1:FP:am:0:d6_15:INDEL:het	1|1:FN:am:.:d6_15:INDEL:homalt	0/1:FP:am:227.61:d6_15:INDEL:het	1|1:FN:am:.:d6_15:INDEL:homalt	0/1:FP:am:10:d6_15:INDEL:het	19:54399630	53896376
Common		GRCh38			19	chr19	54399630	53896376	3	FP_FN	GATTATTATT	G	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:d6_15:INDEL:homalt	0/1:FP:am:100:d6_15:INDEL:het	CommonFP_FN			no	yes	benchmark misses haplotype in TR likely due to highly homozygous region													1|1:FN:am:.:d6_15:INDEL:homalt	0/1:FP:am:1354.73:d6_15:INDEL:het	1|1:FN:am:.:d6_15:INDEL:homalt	0/1:FP:am:1456.73:d6_15:INDEL:het	1|1:FN:am:.:d6_15:INDEL:homalt	0/1:FP:am:30:d6_15:INDEL:het	1|1:FN:am:.:d6_15:INDEL:homalt	0/1:FP:am:653.06:d6_15:INDEL:het	1|1:FN:am:.:d6_15:INDEL:homalt	0/1:FP:am:0:d6_15:INDEL:het	1|1:FN:am:.:d6_15:INDEL:homalt	0/1:FP:am:229.3:d6_15:INDEL:het	1|1:FN:am:.:d6_15:INDEL:homalt	0/1:FP:am:10:d6_15:INDEL:het		54399630
Common		GRCh37			19	chr19	54399633	53896379	0	FP	TATTATT	T	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:lm:d6_15:INDEL:het	CommonFP			no	yes	benchmark misses haplotype in TR likely due to highly homozygous region													.:.:.:.:.:NOCALL:nocall	0/1:1354.73:FP:lm:d6_15:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:1538.73:FP:lm:d6_15:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:lm:d6_15:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:1331.06:FP:lm:d6_15:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:lm:d6_15:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:227.61:FP:lm:d6_15:INDEL:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	19:54399633	53896379
Roche	RN_HG002_Illumina_PacBio_Oxford.vcf.gz	GRCh38	small-variants	INDEL	19	chr19	54399633	53896379	0	FP	TATTATT	T	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:lm:d6_15:INDEL:het 	no	yes	It seems to be multi-allelic as we have predicted: chr19-53896376-GATTATTATT-G,GATT. This is also supported from parents	no	yes	benchmark misses haplotype in TR likely due to highly homozygous region																												54399633
Common		GRCh38			19	chr19	54399633	53896379	1066463	FP	TATTATT	T	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:lm:d6_15:INDEL:het	CommonFP			no	yes	benchmark misses haplotype in TR likely due to highly homozygous region													.:.:.:.:.:NOCALL:nocall	0/1:1354.73:FP:lm:d6_15:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:1456.73:FP:lm:d6_15:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:lm:d6_15:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:653.06:FP:lm:d6_15:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:lm:d6_15:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:229.3:FP:lm:d6_15:INDEL:het	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.		54399633
DNAnexus	hs37d5_HG002_WGS_union.vcf.gz	GRCh37	small-variants	SNP	19	chr19	55474210	54962842	5650	FN	G	A	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	yes	no																															19:55474210	54962842
Common		GRCh37			19	chr19	55479860	54968492	0	FP_FN	A	AT	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:100:i1_5:INDEL:het	CommonFP_FN			no	yes	benchmark misses haplotype in homopolymer likely due to fairly homozygous region and/or noisy HiFi reads													1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:368.73:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:306.73:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:30:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:291.64:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:0:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:48.37:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:12:i1_5:INDEL:het	19:55479860	54968492
DNAnexus	GRCh38_HG002_WGS_union.vcf.gz	GRCh38	small-variants	INDEL	19	chr19	55479860	54968492	0	FP_FN	A	AT	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:0:i1_5:INDEL:het 	yes	no	It is surrounding a homopolymer Ts (14 of them). The long read, assembly-based data is more relaiable than short read-based, mapping variant calling	no	yes	benchmark misses haplotype in homopolymer likely due to fairly homozygous region and/or noisy HiFi reads				skip																								55479860
Common		GRCh38			19	chr19	55479860	54968492	8318	FP_FN	A	AT	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:100:i1_5:INDEL:het	CommonFP_FN			no	yes	benchmark misses haplotype in homopolymer likely due to fairly homozygous region and/or noisy HiFi reads													1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:368.73:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:306.73:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:30:i1_5:INDEL:het	1|1:FN:.:.:i1_5:INDEL:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:0:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:48.39:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:12:i1_5:INDEL:het		55479860
Common		GRCh37			19	chr19	55488178	54976810	7675	FP_FN	C	CT,CTTTTTTTTTTTTTTTTTTTT	GT:BD:BK:BI:QQ:BVT:BLT	2|1:TP:gm:i16_plus,i1_5:100:INDEL:hetalt	2/1:TP:gm:i16_plus,i1_5:100:INDEL:hetalt	CommonFP_FN			unsure		good evidence for large ins in long homopolymer on one haplotype, which is in the benchmark, but exact length is unclear													2|1:FN:am:i16_plus,i1_5:.:INDEL:hetalt	1/1:FP:am:i1_5:515.73:INDEL:homalt	2|1:FN:am:i16_plus,i1_5:.:INDEL:hetalt	1/1:FP:am:i1_5:611.73:INDEL:homalt	2|1:FN:am:i16_plus,i1_5:.:INDEL:hetalt	1/1:FP:am:i1_5:30:INDEL:homalt	2|1:FN:am:i16_plus,i1_5:.:INDEL:hetalt	1/1:FP:am:i1_5:597.06:INDEL:homalt	2|1:FN:lm:i16_plus,i1_5:.:INDEL:hetalt	.:.:.:.:0:NOCALL:nocall	2|1:FN:am:i16_plus,i1_5:.:INDEL:hetalt	1/1:FP:am:i1_5:78.41:INDEL:homalt	2|1:FN:am:i16_plus,i1_5:.:INDEL:hetalt	0/1:FP:am:i1_5:8:INDEL:het	19:55488178	54976810
Common		GRCh37			19	chr19	55495853	54984485	0	FP_FN	C	CTTTTTTT,CTTTTTTTT,CTTTTTTTTTTTTTTTTTT	GT:BD:BK:BI:QQ:BVT:BLT	2|1:FN:am:i6_15:.:INDEL:hetalt	1/1:FP:am:i6_15:100:INDEL:homalt	CommonFP_FN			unsure		some evidence for much larger ins in long homopolymer on one haplotype													2|1:FN:.:i6_15:.:INDEL:hetalt	.:.:.:.:0:NOCALL:nocall	2|1:FN:am:i6_15:.:INDEL:hetalt	1/1:FP:am:i6_15:172.74:INDEL:homalt	2|1:FN:am:i6_15:.:INDEL:hetalt	1/1:FP:am:i6_15:30:INDEL:homalt	2|1:FN:lm:i6_15:.:INDEL:hetalt	0/3:FP:lm:i16_plus:11.3:INDEL:het	2|1:FN:am:i6_15:.:INDEL:hetalt	1/1:FP:am:i6_15:0:INDEL:homalt	2|1:FN:am:i6_15:.:INDEL:hetalt	1/1:FP:am:i6_15:115.61:INDEL:homalt	2|1:FN:am:i6_15:.:INDEL:hetalt	1/1:FP:am:i6_15:14:INDEL:homalt	19:55495853	54984485
Common		GRCh38			19	chr19	55495853	54984485	16107	FP_FN	C	CTTTTTTT,CTTTTTTTT	GT:BD:BK:BI:QQ:BVT:BLT	2|1:FN:am:i6_15:.:INDEL:hetalt	1/1:FP:am:i6_15:100:INDEL:homalt	CommonFP_FN			unsure		some evidence for much larger ins in long homopolymer on one haplotype													2|1:FN:.:i6_15:.:INDEL:hetalt	.:.:.:.:0:NOCALL:nocall	2|1:FN:am:i6_15:.:INDEL:hetalt	1/1:FP:am:i6_15:172.74:INDEL:homalt	2|1:FN:am:i6_15:.:INDEL:hetalt	1/1:FP:am:i6_15:30:INDEL:homalt	2|1:FN:.:i6_15:.:INDEL:hetalt	.:.:.:.:0:NOCALL:nocall	2|1:FN:am:i6_15:.:INDEL:hetalt	1/1:FP:am:i6_15:0:INDEL:homalt	2|1:FN:am:i6_15:.:INDEL:hetalt	1/1:FP:am:i6_15:115.61:INDEL:homalt	2|1:FN:am:i6_15:.:INDEL:hetalt	1/1:FP:am:i6_15:15:INDEL:homalt		55495853
DNAnexus	hs37d5_HG002_WGS_union.vcf.gz	GRCh37	small-variants	INDEL	19	chr19	55511960	55000592	20928	FP	TAA	T	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:lm:d1_5:INDEL:het	unsure	yes	Both the benchmark and the query callset called this deletion. This should not be a FP. Instead, this is just a difference in how to genotype format is presented.	yes	no	benchmark supported by illumina, and query doesn't call both haplotypes correctly																											19:55511960	55000592
Common		GRCh37			19	chr19	55532888	55021520	0	FP_FN	G	GT,GTT	GT:BD:BK:BI:QQ:BVT:BLT	2|1:FN:am:i1_5:.:INDEL:hetalt	1/1:FP:am:i1_5:100:INDEL:homalt	CommonFP_FN			no	yes	likely hifiasm error due to noisy homopolymer													2|1:FN:am:i1_5:.:INDEL:hetalt	1/1:FP:am:i1_5:274.73:INDEL:homalt	2|1:FN:am:i1_5:.:INDEL:hetalt	1/1:FP:am:i1_5:190.73:INDEL:homalt	2|1:FN:am:i1_5:.:INDEL:hetalt	1/1:FP:am:i1_5:30:INDEL:homalt	2|1:FN:am:i1_5:.:INDEL:hetalt	1/1:FP:am:i1_5:374.06:INDEL:homalt	2|1:FN:am:i1_5:.:INDEL:hetalt	1/1:FP:am:i1_5:0:INDEL:homalt	2|1:FN:am:i1_5:.:INDEL:hetalt	1/1:FP:am:i1_5:81.81:INDEL:homalt	2|1:FN:am:i1_5:.:INDEL:hetalt	1/1:FP:am:i1_5:10:INDEL:homalt	19:55532888	55021520
Common		GRCh38			19	chr19	55532888	55021520	116760	FP_FN	G	GT,GTT	GT:BD:BK:BI:QQ:BVT:BLT	2|1:FN:am:i1_5:.:INDEL:hetalt	1/1:FP:am:i1_5:100:INDEL:homalt	CommonFP_FN			no	yes	likely hifiasm error due to noisy homopolymer													2|1:FN:am:i1_5:.:INDEL:hetalt	1/1:FP:am:i1_5:274.73:INDEL:homalt	2|1:FN:am:i1_5:.:INDEL:hetalt	1/1:FP:am:i1_5:190.73:INDEL:homalt	2|1:FN:am:i1_5:.:INDEL:hetalt	1/1:FP:am:i1_5:30:INDEL:homalt	2|1:FN:lm:i1_5:.:INDEL:hetalt	.:.:.:.:0:NOCALL:nocall	2|1:FN:am:i1_5:.:INDEL:hetalt	1/1:FP:am:i1_5:0:INDEL:homalt	2|1:FN:am:i1_5:.:INDEL:hetalt	1/1:FP:am:i1_5:81.81:INDEL:homalt	2|1:FN:am:i1_5:.:INDEL:hetalt	1/1:FP:am:i1_5:10:INDEL:homalt		55532888
Common		GRCh37			19	chr19	55649648	55138280	0	FN	G	GT	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			unsure		likely hifiasm error due to noisy homopolymer but illumina is lower than normal coverage so uncertain													1|0:TP:gm:i1_5:INDEL:het:20.77	0/1:TP:gm:i1_5:INDEL:het:20.77	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	19:55649648	55138280
Common		GRCh38			19	chr19	55649648	55138280	3366293	FN	G	GT	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			unsure		likely hifiasm error due to noisy homopolymer but illumina is lower than normal coverage so uncertain													1|0:TP:gm:i1_5:INDEL:het:20.77	0/1:TP:gm:i1_5:INDEL:het:20.77	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0		55649648
Common		GRCh37			19	chr19	59015940	58504573	5582861	FP_FN	TGG	T,TGGGGG	GT:BD:BK:BI:QQ:BVT:BLT	2|1:FN:am:d1_5,i1_5:.:INDEL:hetalt	0/1:FP:am:d1_5:100:INDEL:het	CommonFP_FN			unsure		all techs noisy in G homopolymer													2|1:FN:am:d1_5,i1_5:.:INDEL:hetalt	0/1:FP:am:d1_5:796.73:INDEL:het	2|1:FN:am:d1_5,i1_5:.:INDEL:hetalt	1/1:FP:am:d1_5:482.73:INDEL:homalt	2|1:FN:am:d1_5,i1_5:.:INDEL:hetalt	1/1:FP:am:d1_5:30:INDEL:homalt	2|1:FN:am:d1_5,i1_5:.:INDEL:hetalt	1/1:FP:am:d1_5:692.03:INDEL:homalt	2|1:FN:.:d1_5,i1_5:.:INDEL:hetalt	.:.:.:.:0:NOCALL:nocall	2|1:FN:am:d1_5,i1_5:.:INDEL:hetalt	0/1:FP:am:d1_5:189.48:INDEL:het	2|1:FN:am:d1_5,i1_5:.:INDEL:hetalt	1/1:FP:am:d1_5:13:INDEL:homalt	19:59015940	58504573
Common		GRCh37			20	chr20	62718787	64087434	0	FN	G	C	GT:BD:BK:BI:BVT:BLT:QQ	1|0:TP:gm:tv:SNP:het:36.989	0/1:TP:gm:tv:SNP:het:36.989	CommonFN			yes	no	missed by short reads in long TR													1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:tv:SNP:het:413.17	0/1:TP:gm:tv:SNP:het:413.17	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	20:62718787	64087434
Common		GRCh38			20	chr20	62718787	64087434	107967	FN	G	C	GT:BD:BK:QQ:BI:BVT:BLT	1|0:TP:gm:100:tv:SNP:het	0/1:TP:gm:100:tv:SNP:het	CommonFN			yes	no	missed by short reads in long TR													1|0:FN:.:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall	1|0:FN:.:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall	1|0:FN:.:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall	1|0:TP:gm:385.69:tv:SNP:het	0/1:TP:gm:385.69:tv:SNP:het	1|0:FN:.:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall	1|0:FN:.:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall	1|0:FN:.:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall		62718787
Common		GRCh37			20	chr20	62826754	64195401	-29748685	FP_FN	C	CTTTTTT,CTTTTTTT	GT:BD:BK:BI:QQ:BVT:BLT	2|1:TP:gm:i6_15:100:INDEL:hetalt	2/1:TP:gm:i6_15:100:INDEL:hetalt	CommonFP_FN			yes	no	good support in illumina for ins in long homopolymer													2|1:FN:am:i6_15:.:INDEL:hetalt	1/1:FP:am:i6_15:2344.73:INDEL:homalt	2|1:FN:am:i6_15:.:INDEL:hetalt	1/1:FP:am:i6_15:536.73:INDEL:homalt	2|1:FN:am:i6_15:.:INDEL:hetalt	2/2:FP:am:i6_15:30:INDEL:homalt	2|1:FN:am:i6_15:.:INDEL:hetalt	0/1:FP:am:i6_15:8.5:INDEL:het	2|1:TP:gm:i6_15:0:INDEL:hetalt	2/1:TP:gm:i6_15:0:INDEL:hetalt	2|1:TP:gm:i6_15:116.13:INDEL:hetalt	2/1:TP:gm:i6_15:116.13:INDEL:hetalt	2|1:FN:am:i6_15:.:INDEL:hetalt	1/1:FP:am:i6_15:18:INDEL:homalt	20:62826754	64195401
Common		GRCh38			21	chr21	35819014	34446716	49	FN	G	A	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	Both haplotypes are missing from HiFi and Illumina reads in KCNE1 because these reads align to an extra copy of the gene (KCNE1B) in GRCh38 that is not in HG002 (and the extra copy is also not in GRCh37, T2T-CHM13, or most individuals)													1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:ti:SNP:het:30	0/1:TP:gm:ti:SNP:het:30	1|0:TP:gm:ti:SNP:het:18.3	0/1:TP:gm:ti:SNP:het:18.3	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0		35819014
Common		GRCh38			21	chr21	35819063	34446765	19	FN	T	C	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:lm:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	Both haplotypes are missing from HiFi and Illumina reads in KCNE1 because these reads align to an extra copy of the gene (KCNE1B) in GRCh38 that is not in HG002 (and the extra copy is also not in GRCh37, T2T-CHM13, or most individuals)													1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:lm:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:ti:SNP:het:30	0/1:TP:gm:ti:SNP:het:30	1|0:TP:gm:ti:SNP:het:19.5	0/1:TP:gm:ti:SNP:het:19.5	1|0:FN:lm:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:lm:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:lm:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0		35819063
Common		GRCh38			21	chr21	35819082	34446784	913	FP_FN	T	C	GT:BD:BK:QQ:BI:BVT:BLT	0|1:FN:am:.:ti:SNP:het	1/1:FP:am:21.8776:ti:SNP:homalt	CommonFP_FN			yes	no	Both haplotypes are missing from HiFi and Illumina reads in KCNE1 because these reads align to an extra copy of the gene (KCNE1B) in GRCh38 that is not in HG002 (and the extra copy is also not in GRCh37, T2T-CHM13, or most individuals)													0|1:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:am:.:ti:SNP:het	1/1:FP:am:799.77:ti:SNP:homalt	0|1:TP:gm:30:ti:SNP:het	0/1:TP:gm:30:ti:SNP:het	0|1:TP:gm:22.9:ti:SNP:het	0/1:TP:gm:22.9:ti:SNP:het	0|1:FN:am:.:ti:SNP:het	1/1:FP:am:0:ti:SNP:homalt	0|1:FN:am:.:ti:SNP:het	1/1:FP:am:52.11:ti:SNP:homalt	0|1:FN:am:.:ti:SNP:het	1/1:FP:am:38:ti:SNP:homalt		35819082
Common		GRCh38			21	chr21	35819995	34447697	329	FN	G	GC	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	Both haplotypes are missing from HiFi and Illumina reads in KCNE1 because these reads align to an extra copy of the gene (KCNE1B) in GRCh38 that is not in HG002 (and the extra copy is also not in GRCh37, T2T-CHM13, or most individuals)													1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:i1_5:INDEL:homalt:30	1/1:TP:gm:i1_5:INDEL:homalt:30	1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0		35819995
Common		GRCh38			21	chr21	35820324	34448026	763	FN	T	C	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	Both haplotypes are missing from HiFi and Illumina reads in KCNE1 because these reads align to an extra copy of the gene (KCNE1B) in GRCh38 that is not in HG002 (and the extra copy is also not in GRCh37, T2T-CHM13, or most individuals)													1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:ti:SNP:het:30	0/1:TP:gm:ti:SNP:het:30	1|0:TP:gm:ti:SNP:het:35.6	0/1:TP:gm:ti:SNP:het:35.6	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0		35820324
Common		GRCh38			21	chr21	35821087	34448789	332	FN	G	A	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	Both haplotypes are missing from HiFi and Illumina reads in KCNE1 because these reads align to an extra copy of the gene (KCNE1B) in GRCh38 that is not in HG002 (and the extra copy is also not in GRCh37, T2T-CHM13, or most individuals)													1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:ti:SNP:het:30	0/1:TP:gm:ti:SNP:het:30	1|0:TP:gm:ti:SNP:het:25.6	0/1:TP:gm:ti:SNP:het:25.6	1|0:FN:lm:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0		35821087
Common		GRCh38			21	chr21	35821419	34449121	692	FN	T	C	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	Both haplotypes are missing from HiFi and Illumina reads in KCNE1 because these reads align to an extra copy of the gene (KCNE1B) in GRCh38 that is not in HG002 (and the extra copy is also not in GRCh37, T2T-CHM13, or most individuals)													1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:ti:SNP:het:30	0/1:TP:gm:ti:SNP:het:30	1|0:TP:gm:ti:SNP:het:19.2	0/1:TP:gm:ti:SNP:het:19.2	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0		35821419
Common		GRCh38			21	chr21	35822111	34449813	159	FN	A	G	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:39.9993:ti:SNP:homalt	1/1:TP:gm:39.9993:ti:SNP:homalt	CommonFN			yes	no	Both haplotypes are missing from HiFi and Illumina reads in KCNE1 because these reads align to an extra copy of the gene (KCNE1B) in GRCh38 that is not in HG002 (and the extra copy is also not in GRCh37, T2T-CHM13, or most individuals)													1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:TP:gm:30:ti:SNP:homalt	1/1:TP:gm:30:ti:SNP:homalt	1|1:TP:gm:44.1:ti:SNP:homalt	1/1:TP:gm:44.1:ti:SNP:homalt	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall		35822111
Common		GRCh38			21	chr21	35822270	34449972	98	FN	T	C	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:22.3715:ti:SNP:homalt	1/1:TP:gm:22.3715:ti:SNP:homalt	CommonFN			yes	no	Both haplotypes are missing from HiFi and Illumina reads in KCNE1 because these reads align to an extra copy of the gene (KCNE1B) in GRCh38 that is not in HG002 (and the extra copy is also not in GRCh37, T2T-CHM13, or most individuals)													1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:TP:gm:30:ti:SNP:homalt	1/1:TP:gm:30:ti:SNP:homalt	1|1:TP:gm:41:ti:SNP:homalt	1/1:TP:gm:41:ti:SNP:homalt	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall		35822270
Common		GRCh38			21	chr21	35822368	34450070	390	FN	C	T	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:36.989:ti:SNP:homalt	1/1:TP:gm:36.989:ti:SNP:homalt	CommonFN			yes	no	Both haplotypes are missing from HiFi and Illumina reads in KCNE1 because these reads align to an extra copy of the gene (KCNE1B) in GRCh38 that is not in HG002 (and the extra copy is also not in GRCh37, T2T-CHM13, or most individuals)													1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:TP:gm:30:ti:SNP:homalt	1/1:TP:gm:30:ti:SNP:homalt	1|1:TP:gm:35.4:ti:SNP:homalt	1/1:TP:gm:35.4:ti:SNP:homalt	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall		35822368
Common		GRCh38			21	chr21	35822758	34450460	1021	FN	T	C	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	Both haplotypes are missing from HiFi and Illumina reads in KCNE1 because these reads align to an extra copy of the gene (KCNE1B) in GRCh38 that is not in HG002 (and the extra copy is also not in GRCh37, T2T-CHM13, or most individuals)													1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:ti:SNP:het:30	0/1:TP:gm:ti:SNP:het:30	1|0:TP:gm:ti:SNP:het:28.3	0/1:TP:gm:ti:SNP:het:28.3	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0		35822758
Common		GRCh38			21	chr21	35823779	34451481	451	FN	G	A	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:33.98:ti:SNP:homalt	1/1:TP:gm:33.98:ti:SNP:homalt	CommonFN			yes	no	Both haplotypes are missing from HiFi and Illumina reads in KCNE1 because these reads align to an extra copy of the gene (KCNE1B) in GRCh38 that is not in HG002 (and the extra copy is also not in GRCh37, T2T-CHM13, or most individuals)													1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:TP:gm:30:ti:SNP:homalt	1/1:TP:gm:30:ti:SNP:homalt	1|1:TP:gm:43.4:ti:SNP:homalt	1/1:TP:gm:43.4:ti:SNP:homalt	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall		35823779
Common		GRCh38			21	chr21	35824230	34451932	238	FN	T	C	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:100:ti:SNP:homalt	1/1:TP:gm:100:ti:SNP:homalt	CommonFN			yes	no	Both haplotypes are missing from HiFi and Illumina reads in KCNE1 because these reads align to an extra copy of the gene (KCNE1B) in GRCh38 that is not in HG002 (and the extra copy is also not in GRCh37, T2T-CHM13, or most individuals)													1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:TP:gm:30:ti:SNP:homalt	1/1:TP:gm:30:ti:SNP:homalt	1|1:TP:gm:39:ti:SNP:homalt	1/1:TP:gm:39:ti:SNP:homalt	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall		35824230
Common		GRCh38			21	chr21	35824468	34452170	134	FN	G	A	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:100:ti:SNP:homalt	1/1:TP:gm:100:ti:SNP:homalt	CommonFN			yes	no	Both haplotypes are missing from HiFi and Illumina reads in KCNE1 because these reads align to an extra copy of the gene (KCNE1B) in GRCh38 that is not in HG002 (and the extra copy is also not in GRCh37, T2T-CHM13, or most individuals)													1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:TP:gm:30:ti:SNP:homalt	1/1:TP:gm:30:ti:SNP:homalt	1|1:TP:gm:34.4:ti:SNP:homalt	1/1:TP:gm:34.4:ti:SNP:homalt	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall		35824468
Common		GRCh38			21	chr21	35824602	34452304	434	FN	T	C	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:100:ti:SNP:homalt	1/1:TP:gm:100:ti:SNP:homalt	CommonFN			yes	no	Both haplotypes are missing from HiFi and Illumina reads in KCNE1 because these reads align to an extra copy of the gene (KCNE1B) in GRCh38 that is not in HG002 (and the extra copy is also not in GRCh37, T2T-CHM13, or most individuals)													1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:TP:gm:30:ti:SNP:homalt	1/1:TP:gm:30:ti:SNP:homalt	1|1:TP:gm:43.5:ti:SNP:homalt	1/1:TP:gm:43.5:ti:SNP:homalt	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall		35824602
Common		GRCh38			21	chr21	35825036	34452738	64	FN	GT	G	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	Both haplotypes are missing from HiFi and Illumina reads in KCNE1 because these reads align to an extra copy of the gene (KCNE1B) in GRCh38 that is not in HG002 (and the extra copy is also not in GRCh37, T2T-CHM13, or most individuals)													1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:d1_5:INDEL:het:30	0/1:TP:gm:d1_5:INDEL:het:30	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0		35825036
Common		GRCh38			21	chr21	35825100	34452802	166	FN	A	C	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:14.5683:tv:SNP:homalt	1/1:TP:gm:14.5683:tv:SNP:homalt	CommonFN			yes	no	Both haplotypes are missing from HiFi and Illumina reads in KCNE1 because these reads align to an extra copy of the gene (KCNE1B) in GRCh38 that is not in HG002 (and the extra copy is also not in GRCh37, T2T-CHM13, or most individuals)													1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:TP:gm:30:tv:SNP:homalt	1/1:TP:gm:30:tv:SNP:homalt	1|1:TP:gm:47.6:tv:SNP:homalt	1/1:TP:gm:47.6:tv:SNP:homalt	1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall		35825100
Common		GRCh38			21	chr21	35825266	34452968	144	FN	A	G	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:30.4577:ti:SNP:homalt	1/1:TP:gm:30.4577:ti:SNP:homalt	CommonFN			yes	no	Both haplotypes are missing from HiFi and Illumina reads in KCNE1 because these reads align to an extra copy of the gene (KCNE1B) in GRCh38 that is not in HG002 (and the extra copy is also not in GRCh37, T2T-CHM13, or most individuals)													1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:TP:gm:30:ti:SNP:homalt	1/1:TP:gm:30:ti:SNP:homalt	1|1:TP:gm:35.2:ti:SNP:homalt	1/1:TP:gm:35.2:ti:SNP:homalt	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall		35825266
Common		GRCh38			21	chr21	35825410	34453112	268	FN	G	C	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:100:tv:SNP:homalt	1/1:TP:gm:100:tv:SNP:homalt	CommonFN			yes	no	Both haplotypes are missing from HiFi and Illumina reads in KCNE1 because these reads align to an extra copy of the gene (KCNE1B) in GRCh38 that is not in HG002 (and the extra copy is also not in GRCh37, T2T-CHM13, or most individuals)													1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:TP:gm:30:tv:SNP:homalt	1/1:TP:gm:30:tv:SNP:homalt	1|1:TP:gm:40.7:tv:SNP:homalt	1/1:TP:gm:40.7:tv:SNP:homalt	1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall		35825410
Common		GRCh38			21	chr21	35825678	34453380	1098	FN	A	G	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:39.9993:ti:SNP:homalt	1/1:TP:gm:39.9993:ti:SNP:homalt	CommonFN			yes	no	Both haplotypes are missing from HiFi and Illumina reads in KCNE1 because these reads align to an extra copy of the gene (KCNE1B) in GRCh38 that is not in HG002 (and the extra copy is also not in GRCh37, T2T-CHM13, or most individuals)													1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:TP:gm:30:ti:SNP:homalt	1/1:TP:gm:30:ti:SNP:homalt	1|1:TP:gm:44.8:ti:SNP:homalt	1/1:TP:gm:44.8:ti:SNP:homalt	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall		35825678
Common		GRCh38			21	chr21	35826776	34454478	101	FN	A	G	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:100:ti:SNP:homalt	1/1:TP:gm:100:ti:SNP:homalt	CommonFN			yes	no	Both haplotypes are missing from HiFi and Illumina reads in KCNE1 because these reads align to an extra copy of the gene (KCNE1B) in GRCh38 that is not in HG002 (and the extra copy is also not in GRCh37, T2T-CHM13, or most individuals)													1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:TP:gm:30:ti:SNP:homalt	1/1:TP:gm:30:ti:SNP:homalt	1|1:TP:gm:27.6:ti:SNP:homalt	1/1:TP:gm:27.6:ti:SNP:homalt	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall		35826776
Common		GRCh38			21	chr21	35826877	34454579	306	FN	C	T	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:100:ti:SNP:homalt	1/1:TP:gm:100:ti:SNP:homalt	CommonFN			yes	no	Both haplotypes are missing from HiFi and Illumina reads in KCNE1 because these reads align to an extra copy of the gene (KCNE1B) in GRCh38 that is not in HG002 (and the extra copy is also not in GRCh37, T2T-CHM13, or most individuals)													1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:TP:gm:30:ti:SNP:homalt	1/1:TP:gm:30:ti:SNP:homalt	1|1:TP:gm:39:ti:SNP:homalt	1/1:TP:gm:39:ti:SNP:homalt	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall		35826877
Common		GRCh38			21	chr21	35827183	34454885	190	FN	A	G	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:100:ti:SNP:homalt	1/1:TP:gm:100:ti:SNP:homalt	CommonFN			yes	no	Both haplotypes are missing from HiFi and Illumina reads in KCNE1 because these reads align to an extra copy of the gene (KCNE1B) in GRCh38 that is not in HG002 (and the extra copy is also not in GRCh37, T2T-CHM13, or most individuals)													1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:TP:gm:30:ti:SNP:homalt	1/1:TP:gm:30:ti:SNP:homalt	1|1:TP:gm:47.1:ti:SNP:homalt	1/1:TP:gm:47.1:ti:SNP:homalt	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall		35827183
Common		GRCh38			21	chr21	35827373	34455075	58	FN	C	T	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:100:ti:SNP:homalt	1/1:TP:gm:100:ti:SNP:homalt	CommonFN			yes	no	Both haplotypes are missing from HiFi and Illumina reads in KCNE1 because these reads align to an extra copy of the gene (KCNE1B) in GRCh38 that is not in HG002 (and the extra copy is also not in GRCh37, T2T-CHM13, or most individuals)													1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:TP:gm:30:ti:SNP:homalt	1/1:TP:gm:30:ti:SNP:homalt	1|1:TP:gm:42.8:ti:SNP:homalt	1/1:TP:gm:42.8:ti:SNP:homalt	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall		35827373
Common		GRCh38			21	chr21	35827431	34455133	49	FN	A	G	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:21.1389:ti:SNP:homalt	1/1:TP:gm:21.1389:ti:SNP:homalt	CommonFN			yes	no	Both haplotypes are missing from HiFi and Illumina reads in KCNE1 because these reads align to an extra copy of the gene (KCNE1B) in GRCh38 that is not in HG002 (and the extra copy is also not in GRCh37, T2T-CHM13, or most individuals)													1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:TP:gm:30:ti:SNP:homalt	1/1:TP:gm:30:ti:SNP:homalt	1|1:TP:gm:36.6:ti:SNP:homalt	1/1:TP:gm:36.6:ti:SNP:homalt	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall		35827431
Common		GRCh38			21	chr21	35827480	34455182	990	FN	T	TA	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	Both haplotypes are missing from HiFi and Illumina reads in KCNE1 because these reads align to an extra copy of the gene (KCNE1B) in GRCh38 that is not in HG002 (and the extra copy is also not in GRCh37, T2T-CHM13, or most individuals)													1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:i1_5:INDEL:homalt:30	1/1:TP:gm:i1_5:INDEL:homalt:30	1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0		35827480
Common		GRCh38			21	chr21	35828470	34456172	600	FN	C	G	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:100:tv:SNP:homalt	1/1:TP:gm:100:tv:SNP:homalt	CommonFN			yes	no	Both haplotypes are missing from HiFi and Illumina reads in KCNE1 because these reads align to an extra copy of the gene (KCNE1B) in GRCh38 that is not in HG002 (and the extra copy is also not in GRCh37, T2T-CHM13, or most individuals)													1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:TP:gm:30:tv:SNP:homalt	1/1:TP:gm:30:tv:SNP:homalt	1|1:TP:gm:42.3:tv:SNP:homalt	1/1:TP:gm:42.3:tv:SNP:homalt	1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall		35828470
Common		GRCh38			21	chr21	35829070	34456772	149	FN	C	A	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:100:tv:SNP:homalt	1/1:TP:gm:100:tv:SNP:homalt	CommonFN			yes	no	Both haplotypes are missing from HiFi and Illumina reads in KCNE1 because these reads align to an extra copy of the gene (KCNE1B) in GRCh38 that is not in HG002 (and the extra copy is also not in GRCh37, T2T-CHM13, or most individuals)													1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:TP:gm:30:tv:SNP:homalt	1/1:TP:gm:30:tv:SNP:homalt	1|1:TP:gm:42:tv:SNP:homalt	1/1:TP:gm:42:tv:SNP:homalt	1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall		35829070
Common		GRCh38			21	chr21	35829219	34456921	15	FN	C	T	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:100:ti:SNP:homalt	1/1:TP:gm:100:ti:SNP:homalt	CommonFN			yes	no	Both haplotypes are missing from HiFi and Illumina reads in KCNE1 because these reads align to an extra copy of the gene (KCNE1B) in GRCh38 that is not in HG002 (and the extra copy is also not in GRCh37, T2T-CHM13, or most individuals)													1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:TP:gm:30:ti:SNP:homalt	1/1:TP:gm:30:ti:SNP:homalt	1|1:TP:gm:40.6:ti:SNP:homalt	1/1:TP:gm:40.6:ti:SNP:homalt	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall		35829219
Common		GRCh38			21	chr21	35829234	34456936	470	FN	G	T	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:100:tv:SNP:homalt	1/1:TP:gm:100:tv:SNP:homalt	CommonFN			yes	no	Both haplotypes are missing from HiFi and Illumina reads in KCNE1 because these reads align to an extra copy of the gene (KCNE1B) in GRCh38 that is not in HG002 (and the extra copy is also not in GRCh37, T2T-CHM13, or most individuals)													1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:TP:gm:30:tv:SNP:homalt	1/1:TP:gm:30:tv:SNP:homalt	1|1:TP:gm:39.5:tv:SNP:homalt	1/1:TP:gm:39.5:tv:SNP:homalt	1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall		35829234
Common		GRCh38			21	chr21	35829704	34457406	78	FN	C	T	GT:BD:BK:QQ:BI:BVT:BLT	0|1:TP:gm:100:ti:SNP:het	0/1:TP:gm:100:ti:SNP:het	CommonFN			yes	no	Both haplotypes are missing from HiFi and Illumina reads in KCNE1 because these reads align to an extra copy of the gene (KCNE1B) in GRCh38 that is not in HG002 (and the extra copy is also not in GRCh37, T2T-CHM13, or most individuals)													0|1:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:TP:gm:30:ti:SNP:het	0/1:TP:gm:30:ti:SNP:het	0|1:TP:gm:35.9:ti:SNP:het	0/1:TP:gm:35.9:ti:SNP:het	0|1:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall		35829704
Common		GRCh38			21	chr21	35829782	34457484	76	FN	T	C	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:100:ti:SNP:homalt	1/1:TP:gm:100:ti:SNP:homalt	CommonFN			yes	no	Both haplotypes are missing from HiFi and Illumina reads in KCNE1 because these reads align to an extra copy of the gene (KCNE1B) in GRCh38 that is not in HG002 (and the extra copy is also not in GRCh37, T2T-CHM13, or most individuals)													1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:TP:gm:30:ti:SNP:homalt	1/1:TP:gm:30:ti:SNP:homalt	1|1:TP:gm:37.3:ti:SNP:homalt	1/1:TP:gm:37.3:ti:SNP:homalt	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall		35829782
Common		GRCh38			21	chr21	35829858	34457560	27	FN	A	G	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:100:ti:SNP:homalt	1/1:TP:gm:100:ti:SNP:homalt	CommonFN			yes	no	Both haplotypes are missing from HiFi and Illumina reads in KCNE1 because these reads align to an extra copy of the gene (KCNE1B) in GRCh38 that is not in HG002 (and the extra copy is also not in GRCh37, T2T-CHM13, or most individuals)													1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:TP:gm:30:ti:SNP:homalt	1/1:TP:gm:30:ti:SNP:homalt	1|1:TP:gm:42.7:ti:SNP:homalt	1/1:TP:gm:42.7:ti:SNP:homalt	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall		35829858
PacBio_gatk4	gatk4hc_HG002_15kb_20kb_53X_SequelII.vcf.gz	GRCh38	small-variants	SNP	21	chr21	35829885	34457587	0	FN	G	T	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0	yes	unsure	no alignments for HiFi	yes	no	Both haplotypes are missing from HiFi and Illumina reads in KCNE1 because these reads align to an extra copy of the gene (KCNE1B) in GRCh38 that is not in HG002 (and the extra copy is also not in GRCh37, T2T-CHM13, or most individuals)																												35829885
Common		GRCh38			21	chr21	35829885	34457587	1930	FN	G	T	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:100:tv:SNP:homalt	1/1:TP:gm:100:tv:SNP:homalt	CommonFN			yes	no	Both haplotypes are missing from HiFi and Illumina reads in KCNE1 because these reads align to an extra copy of the gene (KCNE1B) in GRCh38 that is not in HG002 (and the extra copy is also not in GRCh37, T2T-CHM13, or most individuals)													1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:TP:gm:30:tv:SNP:homalt	1/1:TP:gm:30:tv:SNP:homalt	1|1:TP:gm:42.6:tv:SNP:homalt	1/1:TP:gm:42.6:tv:SNP:homalt	1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall		35829885
Common		GRCh38			21	chr21	35831815	34459517	520	FN	A	C	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:100:tv:SNP:homalt	1/1:TP:gm:100:tv:SNP:homalt	CommonFN			yes	no	Both haplotypes are missing from HiFi and Illumina reads in KCNE1 because these reads align to an extra copy of the gene (KCNE1B) in GRCh38 that is not in HG002 (and the extra copy is also not in GRCh37, T2T-CHM13, or most individuals)													1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:TP:gm:30:tv:SNP:homalt	1/1:TP:gm:30:tv:SNP:homalt	1|1:TP:gm:39.6:tv:SNP:homalt	1/1:TP:gm:39.6:tv:SNP:homalt	1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall		35831815
Common		GRCh38			21	chr21	35832335	34460037	1208	FN	G	A	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:100:ti:SNP:homalt	1/1:TP:gm:100:ti:SNP:homalt	CommonFN			yes	no	Both haplotypes are missing from HiFi and Illumina reads in KCNE1 because these reads align to an extra copy of the gene (KCNE1B) in GRCh38 that is not in HG002 (and the extra copy is also not in GRCh37, T2T-CHM13, or most individuals)													1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:TP:gm:30:ti:SNP:homalt	1/1:TP:gm:30:ti:SNP:homalt	1|1:TP:gm:46.8:ti:SNP:homalt	1/1:TP:gm:46.8:ti:SNP:homalt	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall		35832335
Common		GRCh38			21	chr21	35833543	34461245	784	FN	G	A	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:29.2094:ti:SNP:homalt	1/1:TP:gm:29.2094:ti:SNP:homalt	CommonFN			yes	no	Both haplotypes are missing from HiFi and Illumina reads in KCNE1 because these reads align to an extra copy of the gene (KCNE1B) in GRCh38 that is not in HG002 (and the extra copy is also not in GRCh37, T2T-CHM13, or most individuals)													1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:TP:gm:30:ti:SNP:homalt	1/1:TP:gm:30:ti:SNP:homalt	1|1:TP:gm:40.8:ti:SNP:homalt	1/1:TP:gm:40.8:ti:SNP:homalt	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall		35833543
Common		GRCh38			21	chr21	35834327	34462029	1203	FN	C	T	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:100:ti:SNP:homalt	1/1:TP:gm:100:ti:SNP:homalt	CommonFN			yes	no	Both haplotypes are missing from HiFi and Illumina reads in KCNE1 because these reads align to an extra copy of the gene (KCNE1B) in GRCh38 that is not in HG002 (and the extra copy is also not in GRCh37, T2T-CHM13, or most individuals)													1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:TP:gm:30:ti:SNP:homalt	1/1:TP:gm:30:ti:SNP:homalt	1|1:TP:gm:44.4:ti:SNP:homalt	1/1:TP:gm:44.4:ti:SNP:homalt	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall		35834327
NYGC	HG-002-2x250-b38.recalibrated.haplotypeCalls.vcf.gz	GRCh38	small-variants	INDEL	21	chr21	35835530	34463232	0	FN	C	CT	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0 	yes	no	variant is in the 2x250 Illumina bam but not called	yes	no	Both haplotypes are missing from HiFi and Illumina reads in KCNE1 because these reads align to an extra copy of the gene (KCNE1B) in GRCh38 that is not in HG002 (and the extra copy is also not in GRCh37, T2T-CHM13, or most individuals)				skip																								35835530
Common		GRCh38			21	chr21	35835530	34463232	59	FN	C	CT	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	Both haplotypes are missing from HiFi and Illumina reads in KCNE1 because these reads align to an extra copy of the gene (KCNE1B) in GRCh38 that is not in HG002 (and the extra copy is also not in GRCh37, T2T-CHM13, or most individuals)													1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:i1_5:INDEL:homalt:30	1/1:TP:gm:i1_5:INDEL:homalt:30	1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0		35835530
Common		GRCh38			21	chr21	35835589	34463291	46	FN	C	T	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:100:ti:SNP:homalt	1/1:TP:gm:100:ti:SNP:homalt	CommonFN			yes	no	Both haplotypes are missing from HiFi and Illumina reads in KCNE1 because these reads align to an extra copy of the gene (KCNE1B) in GRCh38 that is not in HG002 (and the extra copy is also not in GRCh37, T2T-CHM13, or most individuals)													1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:TP:gm:30:ti:SNP:homalt	1/1:TP:gm:30:ti:SNP:homalt	1|1:TP:gm:56.7:ti:SNP:homalt	1/1:TP:gm:56.7:ti:SNP:homalt	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall		35835589
Common		GRCh38			21	chr21	35835635	34463337	522	FN	C	T	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:100:ti:SNP:homalt	1/1:TP:gm:100:ti:SNP:homalt	CommonFN			yes	no	Both haplotypes are missing from HiFi and Illumina reads in KCNE1 because these reads align to an extra copy of the gene (KCNE1B) in GRCh38 that is not in HG002 (and the extra copy is also not in GRCh37, T2T-CHM13, or most individuals)													1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:TP:gm:30:ti:SNP:homalt	1/1:TP:gm:30:ti:SNP:homalt	1|1:TP:gm:44.6:ti:SNP:homalt	1/1:TP:gm:44.6:ti:SNP:homalt	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall		35835635
Common		GRCh38			21	chr21	35836157	34463859	541	FN	T	A	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:100:tv:SNP:homalt	1/1:TP:gm:100:tv:SNP:homalt	CommonFN			yes	no	Both haplotypes are missing from HiFi and Illumina reads in KCNE1 because these reads align to an extra copy of the gene (KCNE1B) in GRCh38 that is not in HG002 (and the extra copy is also not in GRCh37, T2T-CHM13, or most individuals)													1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:TP:gm:30:tv:SNP:homalt	1/1:TP:gm:30:tv:SNP:homalt	1|1:TP:gm:50.5:tv:SNP:homalt	1/1:TP:gm:50.5:tv:SNP:homalt	1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall		35836157
Common		GRCh38			21	chr21	35836698	34464400	1108	FN	A	G	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:39.9993:ti:SNP:homalt	1/1:TP:gm:39.9993:ti:SNP:homalt	CommonFN			yes	no	Both haplotypes are missing from HiFi and Illumina reads in KCNE1 because these reads align to an extra copy of the gene (KCNE1B) in GRCh38 that is not in HG002 (and the extra copy is also not in GRCh37, T2T-CHM13, or most individuals)													1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:TP:gm:30:ti:SNP:homalt	1/1:TP:gm:30:ti:SNP:homalt	1|1:TP:gm:55.8:ti:SNP:homalt	1/1:TP:gm:55.8:ti:SNP:homalt	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall		35836698
Common		GRCh38			21	chr21	35837806	34465508	119	FN	C	T	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:39.9993:ti:SNP:homalt	1/1:TP:gm:39.9993:ti:SNP:homalt	CommonFN			yes	no	Both haplotypes are missing from HiFi and Illumina reads in KCNE1 because these reads align to an extra copy of the gene (KCNE1B) in GRCh38 that is not in HG002 (and the extra copy is also not in GRCh37, T2T-CHM13, or most individuals)													1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:TP:gm:30:ti:SNP:homalt	1/1:TP:gm:30:ti:SNP:homalt	1|1:TP:gm:55:ti:SNP:homalt	1/1:TP:gm:55:ti:SNP:homalt	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall		35837806
Common		GRCh38			21	chr21	35837925	34465627	608	FN	G	A	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:100:ti:SNP:homalt	1/1:TP:gm:100:ti:SNP:homalt	CommonFN			yes	no	Both haplotypes are missing from HiFi and Illumina reads in KCNE1 because these reads align to an extra copy of the gene (KCNE1B) in GRCh38 that is not in HG002 (and the extra copy is also not in GRCh37, T2T-CHM13, or most individuals)													1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:TP:gm:30:ti:SNP:homalt	1/1:TP:gm:30:ti:SNP:homalt	1|1:TP:gm:47.1:ti:SNP:homalt	1/1:TP:gm:47.1:ti:SNP:homalt	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall		35837925
Common		GRCh38			21	chr21	35838533	34466235	374	FN	T	C	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:100:ti:SNP:homalt	1/1:TP:gm:100:ti:SNP:homalt	CommonFN			yes	no	Both haplotypes are missing from HiFi and Illumina reads in KCNE1 because these reads align to an extra copy of the gene (KCNE1B) in GRCh38 that is not in HG002 (and the extra copy is also not in GRCh37, T2T-CHM13, or most individuals)													1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:TP:gm:30:ti:SNP:homalt	1/1:TP:gm:30:ti:SNP:homalt	1|1:TP:gm:42.6:ti:SNP:homalt	1/1:TP:gm:42.6:ti:SNP:homalt	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall		35838533
Common		GRCh38			21	chr21	35838907	34466609	160	FN	G	T	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:100:tv:SNP:homalt	1/1:TP:gm:100:tv:SNP:homalt	CommonFN			yes	no	Both haplotypes are missing from HiFi and Illumina reads in KCNE1 because these reads align to an extra copy of the gene (KCNE1B) in GRCh38 that is not in HG002 (and the extra copy is also not in GRCh37, T2T-CHM13, or most individuals)													1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:TP:gm:30:tv:SNP:homalt	1/1:TP:gm:30:tv:SNP:homalt	1|1:TP:gm:46.4:tv:SNP:homalt	1/1:TP:gm:46.4:tv:SNP:homalt	1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall		35838907
Common		GRCh38			21	chr21	35839067	34466769	62	FN	C	T	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:100:ti:SNP:homalt	1/1:TP:gm:100:ti:SNP:homalt	CommonFN			yes	no	Both haplotypes are missing from HiFi and Illumina reads in KCNE1 because these reads align to an extra copy of the gene (KCNE1B) in GRCh38 that is not in HG002 (and the extra copy is also not in GRCh37, T2T-CHM13, or most individuals)													1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:TP:gm:30:ti:SNP:homalt	1/1:TP:gm:30:ti:SNP:homalt	1|1:TP:gm:57.1:ti:SNP:homalt	1/1:TP:gm:57.1:ti:SNP:homalt	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall		35839067
Common		GRCh38			21	chr21	35839129	34466831	12	FN	G	T	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:100:tv:SNP:homalt	1/1:TP:gm:100:tv:SNP:homalt	CommonFN			yes	no	Both haplotypes are missing from HiFi and Illumina reads in KCNE1 because these reads align to an extra copy of the gene (KCNE1B) in GRCh38 that is not in HG002 (and the extra copy is also not in GRCh37, T2T-CHM13, or most individuals)													1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:TP:gm:30:tv:SNP:homalt	1/1:TP:gm:30:tv:SNP:homalt	1|1:TP:gm:54.8:tv:SNP:homalt	1/1:TP:gm:54.8:tv:SNP:homalt	1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall		35839129
Common		GRCh38			21	chr21	35839141	34466843	93	FN	C	G	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:100:tv:SNP:homalt	1/1:TP:gm:100:tv:SNP:homalt	CommonFN			yes	no	Both haplotypes are missing from HiFi and Illumina reads in KCNE1 because these reads align to an extra copy of the gene (KCNE1B) in GRCh38 that is not in HG002 (and the extra copy is also not in GRCh37, T2T-CHM13, or most individuals)													1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:TP:gm:30:tv:SNP:homalt	1/1:TP:gm:30:tv:SNP:homalt	1|1:TP:gm:49.8:tv:SNP:homalt	1/1:TP:gm:49.8:tv:SNP:homalt	1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall		35839141
NYGC	HG-002-2x250-b38.recalibrated.haplotypeCalls.vcf.gz	GRCh38	small-variants	SNP	21	chr21	35839234	34466936	0	FN	G	A	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0 	yes	no		yes	no	Both haplotypes are missing from HiFi and Illumina reads in KCNE1 because these reads align to an extra copy of the gene (KCNE1B) in GRCh38 that is not in HG002 (and the extra copy is also not in GRCh37, T2T-CHM13, or most individuals)				skip																								35839234
Common		GRCh38			21	chr21	35839234	34466936	40	FN	G	A	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:100:ti:SNP:homalt	1/1:TP:gm:100:ti:SNP:homalt	CommonFN			yes	no	Both haplotypes are missing from HiFi and Illumina reads in KCNE1 because these reads align to an extra copy of the gene (KCNE1B) in GRCh38 that is not in HG002 (and the extra copy is also not in GRCh37, T2T-CHM13, or most individuals)													1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:TP:gm:30:ti:SNP:homalt	1/1:TP:gm:30:ti:SNP:homalt	1|1:TP:gm:40.3:ti:SNP:homalt	1/1:TP:gm:40.3:ti:SNP:homalt	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall		35839234
Common		GRCh38			21	chr21	35839274	34466976	125	FN	T	C	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:100:ti:SNP:homalt	1/1:TP:gm:100:ti:SNP:homalt	CommonFN			yes	no	Both haplotypes are missing from HiFi and Illumina reads in KCNE1 because these reads align to an extra copy of the gene (KCNE1B) in GRCh38 that is not in HG002 (and the extra copy is also not in GRCh37, T2T-CHM13, or most individuals)													1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:TP:gm:30:ti:SNP:homalt	1/1:TP:gm:30:ti:SNP:homalt	1|1:TP:gm:64.4:ti:SNP:homalt	1/1:TP:gm:64.4:ti:SNP:homalt	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall		35839274
Common		GRCh38			21	chr21	35839399	34467101	224	FN	C	T	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:100:ti:SNP:homalt	1/1:TP:gm:100:ti:SNP:homalt	CommonFN			yes	no	Both haplotypes are missing from HiFi and Illumina reads in KCNE1 because these reads align to an extra copy of the gene (KCNE1B) in GRCh38 that is not in HG002 (and the extra copy is also not in GRCh37, T2T-CHM13, or most individuals)													1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:TP:gm:30:ti:SNP:homalt	1/1:TP:gm:30:ti:SNP:homalt	1|1:TP:gm:42.4:ti:SNP:homalt	1/1:TP:gm:42.4:ti:SNP:homalt	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall		35839399
Common		GRCh38			21	chr21	35839623	34467325	340	FN	C	T	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:100:ti:SNP:homalt	1/1:TP:gm:100:ti:SNP:homalt	CommonFN			yes	no	Both haplotypes are missing from HiFi and Illumina reads in KCNE1 because these reads align to an extra copy of the gene (KCNE1B) in GRCh38 that is not in HG002 (and the extra copy is also not in GRCh37, T2T-CHM13, or most individuals)													1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:TP:gm:30:ti:SNP:homalt	1/1:TP:gm:30:ti:SNP:homalt	1|1:TP:gm:44.4:ti:SNP:homalt	1/1:TP:gm:44.4:ti:SNP:homalt	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall		35839623
Common		GRCh38			21	chr21	35839963	34467665	283	FN	C	T	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:100:ti:SNP:homalt	1/1:TP:gm:100:ti:SNP:homalt	CommonFN			yes	no	Both haplotypes are missing from HiFi and Illumina reads in KCNE1 because these reads align to an extra copy of the gene (KCNE1B) in GRCh38 that is not in HG002 (and the extra copy is also not in GRCh37, T2T-CHM13, or most individuals)													1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:TP:gm:30:ti:SNP:homalt	1/1:TP:gm:30:ti:SNP:homalt	1|1:TP:gm:44.4:ti:SNP:homalt	1/1:TP:gm:44.4:ti:SNP:homalt	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall		35839963
Common		GRCh38			21	chr21	35840246	34467948	940	FN	C	CA	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	Both haplotypes are missing from HiFi and Illumina reads in KCNE1 because these reads align to an extra copy of the gene (KCNE1B) in GRCh38 that is not in HG002 (and the extra copy is also not in GRCh37, T2T-CHM13, or most individuals)													1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:i1_5:INDEL:homalt:30	1/1:TP:gm:i1_5:INDEL:homalt:30	1|1:TP:gm:i1_5:INDEL:homalt:41.3	1/1:TP:gm:i1_5:INDEL:homalt:41.3	1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0		35840246
Common		GRCh38			21	chr21	35841186	34468888	142	FN	T	C	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:100:ti:SNP:homalt	1/1:TP:gm:100:ti:SNP:homalt	CommonFN			yes	no	Both haplotypes are missing from HiFi and Illumina reads in KCNE1 because these reads align to an extra copy of the gene (KCNE1B) in GRCh38 that is not in HG002 (and the extra copy is also not in GRCh37, T2T-CHM13, or most individuals)													1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:TP:gm:30:ti:SNP:homalt	1/1:TP:gm:30:ti:SNP:homalt	1|1:TP:gm:47.9:ti:SNP:homalt	1/1:TP:gm:47.9:ti:SNP:homalt	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall		35841186
Common		GRCh38			21	chr21	35841328	34469030	412	FN	A	AAAACAAACAAAC	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:.:i6_15:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	Both haplotypes are missing from HiFi and Illumina reads in KCNE1 because these reads align to an extra copy of the gene (KCNE1B) in GRCh38 that is not in HG002 (and the extra copy is also not in GRCh37, T2T-CHM13, or most individuals)													1|1:FN:.:i6_15:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:i6_15:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:i6_15:INDEL:homalt:30	1/1:TP:gm:i6_15:INDEL:homalt:30	1|1:TP:gm:i6_15:INDEL:homalt:21.3	1/1:TP:gm:i6_15:INDEL:homalt:21.3	1|1:FN:.:i6_15:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:i6_15:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:i6_15:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0		35841328
Common		GRCh38			21	chr21	35841740	34469442	3745	FN	C	A	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:100:tv:SNP:homalt	1/1:TP:gm:100:tv:SNP:homalt	CommonFN			yes	no	Both haplotypes are missing from HiFi and Illumina reads in KCNE1 because these reads align to an extra copy of the gene (KCNE1B) in GRCh38 that is not in HG002 (and the extra copy is also not in GRCh37, T2T-CHM13, or most individuals)													1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:TP:gm:30:tv:SNP:homalt	1/1:TP:gm:30:tv:SNP:homalt	1|1:TP:gm:56.3:tv:SNP:homalt	1/1:TP:gm:56.3:tv:SNP:homalt	1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall		35841740
Common		GRCh38			21	chr21	35845485	34473187	160	FN	G	C	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:100:tv:SNP:homalt	1/1:TP:gm:100:tv:SNP:homalt	CommonFN			yes	no	Both haplotypes are missing from HiFi and Illumina reads in KCNE1 because these reads align to an extra copy of the gene (KCNE1B) in GRCh38 that is not in HG002 (and the extra copy is also not in GRCh37, T2T-CHM13, or most individuals)													1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:TP:gm:30:tv:SNP:homalt	1/1:TP:gm:30:tv:SNP:homalt	1|1:TP:gm:53.2:tv:SNP:homalt	1/1:TP:gm:53.2:tv:SNP:homalt	1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall		35845485
Common		GRCh38			21	chr21	35845645	34473347	126	FN	A	G	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:100:ti:SNP:homalt	1/1:TP:gm:100:ti:SNP:homalt	CommonFN			yes	no	Both haplotypes are missing from HiFi and Illumina reads in KCNE1 because these reads align to an extra copy of the gene (KCNE1B) in GRCh38 that is not in HG002 (and the extra copy is also not in GRCh37, T2T-CHM13, or most individuals)													1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:TP:gm:30:ti:SNP:homalt	1/1:TP:gm:30:ti:SNP:homalt	1|1:TP:gm:44.4:ti:SNP:homalt	1/1:TP:gm:44.4:ti:SNP:homalt	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall		35845645
Common		GRCh38			21	chr21	35845771	34473473	52	FN	G	A	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:33.0111:ti:SNP:homalt	1/1:TP:gm:33.0111:ti:SNP:homalt	CommonFN			yes	no	Both haplotypes are missing from HiFi and Illumina reads in KCNE1 because these reads align to an extra copy of the gene (KCNE1B) in GRCh38 that is not in HG002 (and the extra copy is also not in GRCh37, T2T-CHM13, or most individuals)													1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:TP:gm:30:ti:SNP:homalt	1/1:TP:gm:30:ti:SNP:homalt	1|1:TP:gm:46.1:ti:SNP:homalt	1/1:TP:gm:46.1:ti:SNP:homalt	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall		35845771
Common		GRCh38			21	chr21	35845823	34473525	208	FN	C	T	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:100:ti:SNP:homalt	1/1:TP:gm:100:ti:SNP:homalt	CommonFN			yes	no	Both haplotypes are missing from HiFi and Illumina reads in KCNE1 because these reads align to an extra copy of the gene (KCNE1B) in GRCh38 that is not in HG002 (and the extra copy is also not in GRCh37, T2T-CHM13, or most individuals)													1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:TP:gm:30:ti:SNP:homalt	1/1:TP:gm:30:ti:SNP:homalt	1|1:TP:gm:41.3:ti:SNP:homalt	1/1:TP:gm:41.3:ti:SNP:homalt	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall		35845823
Common		GRCh38			21	chr21	35846031	34473733	1183	FN	C	A	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:100:tv:SNP:homalt	1/1:TP:gm:100:tv:SNP:homalt	CommonFN			yes	no	Both haplotypes are missing from HiFi and Illumina reads in KCNE1 because these reads align to an extra copy of the gene (KCNE1B) in GRCh38 that is not in HG002 (and the extra copy is also not in GRCh37, T2T-CHM13, or most individuals)													1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:TP:gm:30:tv:SNP:homalt	1/1:TP:gm:30:tv:SNP:homalt	1|1:TP:gm:42.4:tv:SNP:homalt	1/1:TP:gm:42.4:tv:SNP:homalt	1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall		35846031
Common		GRCh38			21	chr21	35847214	34474916	925	FN	G	A	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:100:ti:SNP:homalt	1/1:TP:gm:100:ti:SNP:homalt	CommonFN			yes	no	Both haplotypes are missing from HiFi and Illumina reads in KCNE1 because these reads align to an extra copy of the gene (KCNE1B) in GRCh38 that is not in HG002 (and the extra copy is also not in GRCh37, T2T-CHM13, or most individuals)													1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:TP:gm:30:ti:SNP:homalt	1/1:TP:gm:30:ti:SNP:homalt	1|1:TP:gm:51.9:ti:SNP:homalt	1/1:TP:gm:51.9:ti:SNP:homalt	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall		35847214
Roche	RN_HG002_Illumina_PacBio_Oxford.vcf.gz	GRCh38	small-variants	INDEL	21	chr21	35848139	34475841	0	FN	GA	G	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0 	yes	no		yes	no	Both haplotypes are missing from HiFi and Illumina reads in KCNE1 because these reads align to an extra copy of the gene (KCNE1B) in GRCh38 that is not in HG002 (and the extra copy is also not in GRCh37, T2T-CHM13, or most individuals)				skip																								35848139
Common		GRCh38			21	chr21	35848139	34475841	771	FN	GA	G	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	Both haplotypes are missing from HiFi and Illumina reads in KCNE1 because these reads align to an extra copy of the gene (KCNE1B) in GRCh38 that is not in HG002 (and the extra copy is also not in GRCh37, T2T-CHM13, or most individuals)													1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:d1_5:INDEL:het:30	0/1:TP:gm:d1_5:INDEL:het:30	1|0:TP:gm:d1_5:INDEL:het:20.3	0/1:TP:gm:d1_5:INDEL:het:20.3	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:d1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0		35848139
Common		GRCh38			21	chr21	35848910	34476612	137	FN	T	A	GT:BD:BK:QQ:BI:BVT:BLT	1|0:TP:gm:100:tv:SNP:het	0/1:TP:gm:100:tv:SNP:het	CommonFN			yes	no	Both haplotypes are missing from HiFi and Illumina reads in KCNE1 because these reads align to an extra copy of the gene (KCNE1B) in GRCh38 that is not in HG002 (and the extra copy is also not in GRCh37, T2T-CHM13, or most individuals)													1|0:FN:.:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall	1|0:FN:.:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall	1|0:TP:gm:30:tv:SNP:het	0/1:TP:gm:30:tv:SNP:het	1|0:TP:gm:67.5:tv:SNP:het	0/1:TP:gm:67.5:tv:SNP:het	1|0:FN:.:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall	1|0:FN:.:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall	1|0:FN:.:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall		35848910
Common		GRCh38			21	chr21	35849047	34476749	300	FN	T	A	GT:BD:BK:QQ:BI:BVT:BLT	1|0:TP:gm:100:tv:SNP:het	0/1:TP:gm:100:tv:SNP:het	CommonFN			yes	no	Both haplotypes are missing from HiFi and Illumina reads in KCNE1 because these reads align to an extra copy of the gene (KCNE1B) in GRCh38 that is not in HG002 (and the extra copy is also not in GRCh37, T2T-CHM13, or most individuals)													1|0:FN:.:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall	1|0:FN:.:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall	1|0:TP:gm:30:tv:SNP:het	0/1:TP:gm:30:tv:SNP:het	1|0:TP:gm:44.5:tv:SNP:het	0/1:TP:gm:44.5:tv:SNP:het	1|0:FN:.:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall	1|0:FN:.:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall	1|0:FN:.:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall		35849047
Common		GRCh38			21	chr21	35849347	34477049	1982	FN	C	CAT	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	Both haplotypes are missing from HiFi and Illumina reads in KCNE1 because these reads align to an extra copy of the gene (KCNE1B) in GRCh38 that is not in HG002 (and the extra copy is also not in GRCh37, T2T-CHM13, or most individuals)													1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:i1_5:INDEL:het:30	0/1:TP:gm:i1_5:INDEL:het:30	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0		35849347
Common		GRCh38			21	chr21	35851329	34479031	719	FN	A	G	GT:BD:BK:QQ:BI:BVT:BLT	1|0:TP:gm:100:ti:SNP:het	0/1:TP:gm:100:ti:SNP:het	CommonFN			yes	no	Both haplotypes are missing from HiFi and Illumina reads in KCNE1 because these reads align to an extra copy of the gene (KCNE1B) in GRCh38 that is not in HG002 (and the extra copy is also not in GRCh37, T2T-CHM13, or most individuals)													1|0:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	1|0:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	1|0:TP:gm:30:ti:SNP:het	0/1:TP:gm:30:ti:SNP:het	1|0:TP:gm:57.4:ti:SNP:het	0/1:TP:gm:57.4:ti:SNP:het	1|0:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	1|0:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	1|0:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall		35851329
Common		GRCh38			21	chr21	35852048	34479750	1128	FN	A	G	GT:BD:BK:QQ:BI:BVT:BLT	0|1:TP:gm:100:ti:SNP:het	0/1:TP:gm:100:ti:SNP:het	CommonFN			yes	no	Both haplotypes are missing from HiFi and Illumina reads in KCNE1 because these reads align to an extra copy of the gene (KCNE1B) in GRCh38 that is not in HG002 (and the extra copy is also not in GRCh37, T2T-CHM13, or most individuals)													0|1:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:TP:gm:30:ti:SNP:het	0/1:TP:gm:30:ti:SNP:het	0|1:TP:gm:44.4:ti:SNP:het	0/1:TP:gm:44.4:ti:SNP:het	0|1:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall		35852048
Common		GRCh38			21	chr21	35853176	34480878	452	FN	T	C	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	Both haplotypes are missing from HiFi and Illumina reads in KCNE1 because these reads align to an extra copy of the gene (KCNE1B) in GRCh38 that is not in HG002 (and the extra copy is also not in GRCh37, T2T-CHM13, or most individuals)													1|0:TP:gm:ti:SNP:het:35.77	0/1:TP:gm:ti:SNP:het:35.77	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:ti:SNP:het:30	0/1:TP:gm:ti:SNP:het:30	1|0:TP:gm:ti:SNP:het:53.1	0/1:TP:gm:ti:SNP:het:53.1	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0		35853176
NYGC	HG-002-2x250-b38.recalibrated.haplotypeCalls.vcf.gz	GRCh38	small-variants	SNP	21	chr21	35853628	34481330	0	FN	T	C	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0 	yes	no		yes	no	Both haplotypes are missing from HiFi and Illumina reads in KCNE1 because these reads align to an extra copy of the gene (KCNE1B) in GRCh38 that is not in HG002 (and the extra copy is also not in GRCh37, T2T-CHM13, or most individuals)				skip																								35853628
Common		GRCh38			21	chr21	35853628	34481330	971	FN	T	C	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	Both haplotypes are missing from HiFi and Illumina reads in KCNE1 because these reads align to an extra copy of the gene (KCNE1B) in GRCh38 that is not in HG002 (and the extra copy is also not in GRCh37, T2T-CHM13, or most individuals)													1|0:TP:gm:ti:SNP:het:80.77	0/1:TP:gm:ti:SNP:het:80.77	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:ti:SNP:het:30	0/1:TP:gm:ti:SNP:het:30	1|0:TP:gm:ti:SNP:het:51	0/1:TP:gm:ti:SNP:het:51	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0		35853628
Common		GRCh38			21	chr21	35854599	34482301	1660130	FN	T	G	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	Both haplotypes are missing from HiFi and Illumina reads in KCNE1 because these reads align to an extra copy of the gene (KCNE1B) in GRCh38 that is not in HG002 (and the extra copy is also not in GRCh37, T2T-CHM13, or most individuals)													1|0:TP:gm:tv:SNP:het:155.77	0/1:TP:gm:tv:SNP:het:155.77	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:tv:SNP:het:30	0/1:TP:gm:tv:SNP:het:30	1|0:TP:gm:tv:SNP:het:50.4	0/1:TP:gm:tv:SNP:het:50.4	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0		35854599
Roche	RN_HG002_Illumina_PacBio_Oxford.vcf.gz	GRCh38	small-variants	INDEL	21	chr21	37514729	36142431	6910884	FP_FN	C	CAAAAAAAAAAAAAA	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:i6_15:INDEL:homalt	0/1:FP:am:100:i6_15:INDEL:het 	yes	no		yes	no	One haplotype is missing from HiFi and Illumina reads in CBS because these reads align to an extra copy of the gene in GRCh38 (CBSL) that is not in HG002 (and CBSL is also not in GRCh37, T2T-CHM13, or most individuals)				skip																								37514729
PacBio_gatk4	gatk4hc_HG002_15kb_20kb_53X_SequelII.vcf.gz	GRCh38	small-variants	SNP	21	chr21	44473425	43053315	21	FP_FN	G	A	GT:BD:BK:QQ:BI:BVT:BLT	1|0:FN:am:.:ti:SNP:het	1/1:FP:am:137.9:ti:SNP:homalt	unsure	unsure	only evidence in LongRanger	yes	no	One haplotype is missing from HiFi and Illumina reads in CBS because these reads align to an extra copy of the gene in GRCh38 (CBSL) that is not in HG002 (and CBSL is also not in GRCh37, T2T-CHM13, or most individuals)																												44473425
PacBio_gatk4	gatk4hc_HG002_15kb_20kb_53X_SequelII.vcf.gz	GRCh38	small-variants	SNP	21	chr21	44473446	43053336	2268	FP_FN	A	G	GT:BD:BK:QQ:BI:BVT:BLT	1|0:FN:am:.:ti:SNP:het	1/1:FP:am:137.9:ti:SNP:homalt	unsure	unsure	only evidence in LongRanger	yes	no	One haplotype is missing from HiFi and Illumina reads in CBS because these reads align to an extra copy of the gene in GRCh38 (CBSL) that is not in HG002 (and CBSL is also not in GRCh37, T2T-CHM13, or most individuals)																												44473446
Roche	RN_HG002_Illumina_PacBio_Oxford.vcf.gz	GRCh38	small-variants	SNP	21	chr21	44475714	43055604	72	FP_FN	T	C	GT:BD:BK:QQ:BI:BVT:BLT	1|0:FN:am:.:ti:SNP:het	1/1:FP:am:100:ti:SNP:homalt 	yes	no	1/1 in Ilmn and PB, only 10x got it	yes	no	One haplotype is missing from HiFi and Illumina reads in CBS because these reads align to an extra copy of the gene in GRCh38 (CBSL) that is not in HG002 (and CBSL is also not in GRCh37, T2T-CHM13, or most individuals)				skip																								44475714
DNAnexus	GRCh38_HG002_WGS_union.vcf.gz	GRCh38	small-variants	SNP	21	chr21	44475786	43055676	0	FP_FN	C	T	GT:BD:BK:QQ:BI:BVT:BLT	1|0:FN:am:.:ti:SNP:het	1/1:FP:am:0:ti:SNP:homalt 	unsure	unsure	10x and ONT indicate Het variant. However, ONT also shows several deletions at this particular position	yes	no	One haplotype is missing from HiFi and Illumina reads in CBS because these reads align to an extra copy of the gene in GRCh38 (CBSL) that is not in HG002 (and CBSL is also not in GRCh37, T2T-CHM13, or most individuals)						likely CBS issue as seen before, single HP for Hifi, few ILMN reads support HOM.  10X has both HP and does appear to support HET.  Nearby variant correlates with reads/HP on ILMN and HiFi. Variant might be correct however GT unsure.																						44475786
NYGC	HG-002-2x250-b38.recalibrated.haplotypeCalls.vcf.gz	GRCh38	small-variants	SNP	21	chr21	44475786	43055676	10	FP_FN	C	T	GT:BD:BK:QQ:BI:BVT:BLT	1|0:FN:am:.:ti:SNP:het	1/1:FP:am:912.77:ti:SNP:homalt 	unsure	yes	Evidence for het genotype is seen in Pacbio hifi assembly and 10X data but there is no evidence in CCS and Illumina, although Illumina has very low coverage at this site. Pacbio CCS reads at this sites have a mapping quality of 254.	yes	no	One haplotype is missing from HiFi and Illumina reads in CBS because these reads align to an extra copy of the gene in GRCh38 (CBSL) that is not in HG002 (and CBSL is also not in GRCh37, T2T-CHM13, or most individuals)																												44475786
NYGC	HG-002-2x250-b38.recalibrated.haplotypeCalls.vcf.gz	GRCh38	small-variants	SNP	21	chr21	44475796	43055686	81	FP_FN	T	C	GT:BD:BK:QQ:BI:BVT:BLT	1|0:FN:am:.:ti:SNP:het	1/1:FP:am:975.77:ti:SNP:homalt 	unsure	yes	Evidence for het genotype only seen in Pacbio Hifi assembly. Pacbio CCS reads at this sites have a mapping quality of 254.	yes	no	One haplotype is missing from HiFi and Illumina reads in CBS because these reads align to an extra copy of the gene in GRCh38 (CBSL) that is not in HG002 (and CBSL is also not in GRCh37, T2T-CHM13, or most individuals)																												44475796
Common		GRCh38			21	chr21	44475877	43055767	882	FN	C	T	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	One haplotype is missing from HiFi and Illumina reads in CBS because these reads align to an extra copy of the gene in GRCh38 (CBSL) that is not in HG002 (and CBSL is also not in GRCh37, T2T-CHM13, or most individuals)													0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:TP:gm:ti:SNP:het:30	0/1:TP:gm:ti:SNP:het:30	0|1:TP:gm:ti:SNP:het:12.8	0/1:TP:gm:ti:SNP:het:12.8	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0		44475877
Common		GRCh38			21	chr21	44476759	43056649	682	FN	A	G	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:100:ti:SNP:homalt	1/1:TP:gm:100:ti:SNP:homalt	CommonFN			yes	no	One haplotype is missing from HiFi and Illumina reads in CBS because these reads align to an extra copy of the gene in GRCh38 (CBSL) that is not in HG002 (and CBSL is also not in GRCh37, T2T-CHM13, or most individuals)													1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:TP:gm:30:ti:SNP:homalt	1/1:TP:gm:30:ti:SNP:homalt	1|1:TP:gm:28.2:ti:SNP:homalt	1/1:TP:gm:28.2:ti:SNP:homalt	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall		44476759
Common		GRCh38			21	chr21	44477441	43057331	2674	FN	G	A	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	One haplotype is missing from HiFi and Illumina reads in CBS because these reads align to an extra copy of the gene in GRCh38 (CBSL) that is not in HG002 (and CBSL is also not in GRCh37, T2T-CHM13, or most individuals)													0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:TP:gm:ti:SNP:het:30	0/1:TP:gm:ti:SNP:het:30	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0		44477441
Common		GRCh38			21	chr21	44480115	43060005	1054	FN	G	T	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	One haplotype is missing from HiFi and Illumina reads in CBS because these reads align to an extra copy of the gene in GRCh38 (CBSL) that is not in HG002 (and CBSL is also not in GRCh37, T2T-CHM13, or most individuals)													0|1:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:TP:gm:tv:SNP:het:30	0/1:TP:gm:tv:SNP:het:30	0|1:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0		44480115
Common		GRCh38			21	chr21	44481169	43061059	355	FN	T	C	GT:BD:BK:QQ:BI:BVT:BLT	1|0:TP:gm:100:ti:SNP:het	0/1:TP:gm:100:ti:SNP:het	CommonFN			yes	no	One haplotype is missing from HiFi and Illumina reads in CBS because these reads align to an extra copy of the gene in GRCh38 (CBSL) that is not in HG002 (and CBSL is also not in GRCh37, T2T-CHM13, or most individuals)													1|0:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	1|0:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	1|0:TP:gm:30:ti:SNP:het	0/1:TP:gm:30:ti:SNP:het	1|0:TP:gm:17.8:ti:SNP:het	0/1:TP:gm:17.8:ti:SNP:het	1|0:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	1|0:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	1|0:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall		44481169
DNAnexus	GRCh38_HG002_WGS_union.vcf.gz	GRCh38	small-variants	INDEL	21	chr21	44481524	43061414	367	FN	C	CT	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0 	yes	no		yes	no	One haplotype is missing from HiFi and Illumina reads in CBS because these reads align to an extra copy of the gene in GRCh38 (CBSL) that is not in HG002 (and CBSL is also not in GRCh37, T2T-CHM13, or most individuals)				skip																								44481524
Common		GRCh38			21	chr21	44481891	43061781	1562	FN	G	A	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	One haplotype is missing from HiFi and Illumina reads in CBS because these reads align to an extra copy of the gene in GRCh38 (CBSL) that is not in HG002 (and CBSL is also not in GRCh37, T2T-CHM13, or most individuals)													0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:TP:gm:ti:SNP:het:30	0/1:TP:gm:ti:SNP:het:30	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0		44481891
BCM-HGSC_xAtlas	HG002.GRCh38.60x.1_merged.vcf.gz	GRCh38	small-variants	SNP	21	chr21	44483453	43063343	319	FP_FN	C	T	GT:BD:BK:QQ:BI:BVT:BLT	1|0:FN:am:.:ti:SNP:het	1/1:FP:am:22:ti:SNP:homalt 	Yes	No		yes	no	One haplotype is missing from HiFi and Illumina reads in CBS because these reads align to an extra copy of the gene in GRCh38 (CBSL) that is not in HG002 (and CBSL is also not in GRCh37, T2T-CHM13, or most individuals)				skip																								44483453
PacBio_gatk4	gatk4hc_HG002_15kb_20kb_53X_SequelII.vcf.gz	GRCh38	small-variants	SNP	21	chr21	44483772	43063662	0	FN	C	T	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	unsure	unsure	only evidence in ONT	yes	no	One haplotype is missing from HiFi and Illumina reads in CBS because these reads align to an extra copy of the gene in GRCh38 (CBSL) that is not in HG002 (and CBSL is also not in GRCh37, T2T-CHM13, or most individuals)																												44483772
Common		GRCh38			21	chr21	44483772	43063662	1578	FN	C	T	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	One haplotype is missing from HiFi and Illumina reads in CBS because these reads align to an extra copy of the gene in GRCh38 (CBSL) that is not in HG002 (and CBSL is also not in GRCh37, T2T-CHM13, or most individuals)													0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:TP:gm:ti:SNP:het:30	0/1:TP:gm:ti:SNP:het:30	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0		44483772
Common		GRCh38			21	chr21	44485350	43065240	921	FN	G	A	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	One haplotype is missing from HiFi and Illumina reads in CBS because these reads align to an extra copy of the gene in GRCh38 (CBSL) that is not in HG002 (and CBSL is also not in GRCh37, T2T-CHM13, or most individuals)													0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:TP:gm:ti:SNP:het:30	0/1:TP:gm:ti:SNP:het:30	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0		44485350
Common		GRCh38			21	chr21	44486271	43066161	53	FN	G	T	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	One haplotype is missing from HiFi and Illumina reads in CBS because these reads align to an extra copy of the gene in GRCh38 (CBSL) that is not in HG002 (and CBSL is also not in GRCh37, T2T-CHM13, or most individuals)													0|1:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:TP:gm:tv:SNP:het:30	0/1:TP:gm:tv:SNP:het:30	0|1:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0		44486271
Common		GRCh38			21	chr21	44486324	43066214	640	FN	T	C	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	One haplotype is missing from HiFi and Illumina reads in CBS because these reads align to an extra copy of the gene in GRCh38 (CBSL) that is not in HG002 (and CBSL is also not in GRCh37, T2T-CHM13, or most individuals)													0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:TP:gm:ti:SNP:het:30	0/1:TP:gm:ti:SNP:het:30	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0		44486324
PacBio_gatk4	gatk4hc_HG002_15kb_20kb_53X_SequelII.vcf.gz	GRCh38	small-variants	SNP	21	chr21	44486964	43066854	0	FN	C	T	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	unsure	unsure	only evidence in LongRanger	yes	no	One haplotype is missing from HiFi and Illumina reads in CBS because these reads align to an extra copy of the gene in GRCh38 (CBSL) that is not in HG002 (and CBSL is also not in GRCh37, T2T-CHM13, or most individuals)																												44486964
Common		GRCh38			21	chr21	44486964	43066854	43	FN	C	T	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	One haplotype is missing from HiFi and Illumina reads in CBS because these reads align to an extra copy of the gene in GRCh38 (CBSL) that is not in HG002 (and CBSL is also not in GRCh37, T2T-CHM13, or most individuals)													0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:TP:gm:ti:SNP:het:30	0/1:TP:gm:ti:SNP:het:30	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0		44486964
Common		GRCh38			21	chr21	44487007	43066897	104	FN	G	A	GT:BD:BK:QQ:BI:BVT:BLT	0|1:TP:gm:10.3388:ti:SNP:het	0/1:TP:gm:10.3388:ti:SNP:het	CommonFN			yes	no	One haplotype is missing from HiFi and Illumina reads in CBS because these reads align to an extra copy of the gene in GRCh38 (CBSL) that is not in HG002 (and CBSL is also not in GRCh37, T2T-CHM13, or most individuals)													0|1:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:TP:gm:30:ti:SNP:het	0/1:TP:gm:30:ti:SNP:het	0|1:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall		44487007
Roche	RN_HG002_Illumina_PacBio_Oxford.vcf.gz	GRCh38	small-variants	SNP	21	chr21	44487111	43067001	0	FN	C	A	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0 	yes	no		yes	no	One haplotype is missing from HiFi and Illumina reads in CBS because these reads align to an extra copy of the gene in GRCh38 (CBSL) that is not in HG002 (and CBSL is also not in GRCh37, T2T-CHM13, or most individuals)				skip																								44487111
Common		GRCh38			21	chr21	44487111	43067001	780	FN	C	A	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	One haplotype is missing from HiFi and Illumina reads in CBS because these reads align to an extra copy of the gene in GRCh38 (CBSL) that is not in HG002 (and CBSL is also not in GRCh37, T2T-CHM13, or most individuals)													0|1:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:TP:gm:tv:SNP:het:30	0/1:TP:gm:tv:SNP:het:30	0|1:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0		44487111
Common		GRCh38			21	chr21	44487891	43067781	504	FN	G	A	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	One haplotype is missing from HiFi and Illumina reads in CBS because these reads align to an extra copy of the gene in GRCh38 (CBSL) that is not in HG002 (and CBSL is also not in GRCh37, T2T-CHM13, or most individuals)													0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:TP:gm:ti:SNP:het:30	0/1:TP:gm:ti:SNP:het:30	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0		44487891
Common		GRCh38			21	chr21	44488395	43068285	360	FN	G	T	GT:BD:BK:QQ:BI:BVT:BLT	0|1:TP:gm:6.3995:tv:SNP:het	0/1:TP:gm:6.3995:tv:SNP:het	CommonFN			yes	no	One haplotype is missing from HiFi and Illumina reads in CBS because these reads align to an extra copy of the gene in GRCh38 (CBSL) that is not in HG002 (and CBSL is also not in GRCh37, T2T-CHM13, or most individuals)													0|1:FN:.:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:.:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:TP:gm:30:tv:SNP:het	0/1:TP:gm:30:tv:SNP:het	0|1:FN:.:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:.:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:.:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:.:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall		44488395
Common		GRCh38			21	chr21	44488755	43068645	358	FN	G	GA	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	One haplotype is missing from HiFi and Illumina reads in CBS because these reads align to an extra copy of the gene in GRCh38 (CBSL) that is not in HG002 (and CBSL is also not in GRCh37, T2T-CHM13, or most individuals)													1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:i1_5:INDEL:homalt:30	1/1:TP:gm:i1_5:INDEL:homalt:30	1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0		44488755
BCM-HGSC_xAtlas	HG002.GRCh38.60x.1_merged.vcf.gz	GRCh38	small-variants	SNP	21	chr21	44489113	43069003	864	FN	T	C	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0 	Yes	No		yes	no	One haplotype is missing from HiFi and Illumina reads in CBS because these reads align to an extra copy of the gene in GRCh38 (CBSL) that is not in HG002 (and CBSL is also not in GRCh37, T2T-CHM13, or most individuals)				skip																								44489113
Common		GRCh38			21	chr21	44489977	43069867	97	FP_FN	G	T	GT:BD:BK:QQ:BI:BVT:BLT	1|0:FN:am:.:tv:SNP:het	1/1:FP:am:100:tv:SNP:homalt	CommonFP_FN			yes	no	One haplotype is missing from HiFi and Illumina reads in CBS because these reads align to an extra copy of the gene in GRCh38 (CBSL) that is not in HG002 (and CBSL is also not in GRCh37, T2T-CHM13, or most individuals)													1|0:FN:.:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall	1|0:FN:am:.:tv:SNP:het	1/1:FP:am:171.8:tv:SNP:homalt	1|0:TP:gm:30:tv:SNP:het	0/1:TP:gm:30:tv:SNP:het	1|0:FN:am:.:tv:SNP:het	1/1:FP:am:12.9:tv:SNP:homalt	1|0:FN:am:.:tv:SNP:het	1/1:FP:am:0:tv:SNP:homalt	1|0:FN:.:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall	1|0:FN:am:.:tv:SNP:het	1/1:FP:am:14:tv:SNP:homalt		44489977
DNAnexus	GRCh38_HG002_WGS_union.vcf.gz	GRCh38	small-variants	SNP	21	chr21	44490074	43069964	140	FP_FN	G	A	GT:BD:BK:QQ:BI:BVT:BLT	1|0:FN:am:.:ti:SNP:het	1/1:FP:am:0:ti:SNP:homalt 	unsure	unsure	10x and ONT show het SNP, while PacBio indicates homozygous variants. Illumina also shows homozygous variants but has only two reads to support this call.	yes	no	One haplotype is missing from HiFi and Illumina reads in CBS because these reads align to an extra copy of the gene in GRCh38 (CBSL) that is not in HG002 (and CBSL is also not in GRCh37, T2T-CHM13, or most individuals)						likely CBS issue as seen before, single HP for Hifi, very few ILMN reads support HOM.  10X has both HP and does appear to support HET.  Nearby variants correlates with reads/HP on ILMN and HiFi. Variant might be correct however GT unsure.																						44490074
Roche	RN_HG002_Illumina_PacBio_Oxford.vcf.gz	GRCh38	small-variants	SNP	21	chr21	44490214	43070104	0	FN	G	T	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0 	yes	no		yes	no	One haplotype is missing from HiFi and Illumina reads in CBS because these reads align to an extra copy of the gene in GRCh38 (CBSL) that is not in HG002 (and CBSL is also not in GRCh37, T2T-CHM13, or most individuals)				skip																								44490214
Common		GRCh38			21	chr21	44490214	43070104	1079	FN	G	T	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	One haplotype is missing from HiFi and Illumina reads in CBS because these reads align to an extra copy of the gene in GRCh38 (CBSL) that is not in HG002 (and CBSL is also not in GRCh37, T2T-CHM13, or most individuals)													0|1:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:TP:gm:tv:SNP:het:30	0/1:TP:gm:tv:SNP:het:30	0|1:TP:gm:tv:SNP:het:4.2	0/1:TP:gm:tv:SNP:het:4.2	0|1:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0		44490214
Common		GRCh38			21	chr21	44491293	43071183	1310	FN	T	C	GT:BD:BK:QQ:BI:BVT:BLT	0|1:TP:gm:39.9993:ti:SNP:het	0/1:TP:gm:39.9993:ti:SNP:het	CommonFN			yes	no	One haplotype is missing from HiFi and Illumina reads in CBS because these reads align to an extra copy of the gene in GRCh38 (CBSL) that is not in HG002 (and CBSL is also not in GRCh37, T2T-CHM13, or most individuals)													0|1:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:TP:gm:30:ti:SNP:het	0/1:TP:gm:30:ti:SNP:het	0|1:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall	0|1:FN:.:.:ti:SNP:het	.:.:.:0:.:NOCALL:nocall		44491293
Common		GRCh38			21	chr21	44492603	43072493	235	FN	C	G	GT:BD:BK:QQ:BI:BVT:BLT	1|0:TP:gm:100:tv:SNP:het	0/1:TP:gm:100:tv:SNP:het	CommonFN			yes	no	One haplotype is missing from HiFi and Illumina reads in CBS because these reads align to an extra copy of the gene in GRCh38 (CBSL) that is not in HG002 (and CBSL is also not in GRCh37, T2T-CHM13, or most individuals)													1|0:FN:.:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall	1|0:FN:.:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall	1|0:TP:gm:30:tv:SNP:het	0/1:TP:gm:30:tv:SNP:het	1|0:TP:gm:14.4:tv:SNP:het	0/1:TP:gm:14.4:tv:SNP:het	1|0:FN:.:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall	1|0:FN:.:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall	1|0:FN:.:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall		44492603
Common		GRCh38			21	chr21	44492838	43072728	3224	FN	C	A	GT:BD:BK:QQ:BI:BVT:BLT	1|0:TP:gm:35.2289:tv:SNP:het	0/1:TP:gm:35.2289:tv:SNP:het	CommonFN			yes	no	One haplotype is missing from HiFi and Illumina reads in CBS because these reads align to an extra copy of the gene in GRCh38 (CBSL) that is not in HG002 (and CBSL is also not in GRCh37, T2T-CHM13, or most individuals)													1|0:FN:.:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall	1|0:FN:.:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall	1|0:TP:gm:30:tv:SNP:het	0/1:TP:gm:30:tv:SNP:het	1|0:FN:.:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall	1|0:FN:.:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall	1|0:FN:.:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall	1|0:FN:.:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall		44492838
BCM-HGSC_xAtlas	HG002.GRCh38.60x.1_merged.vcf.gz	GRCh38	small-variants	SNP	21	chr21	44496062	43075952	0	FN	C	G	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:.:tv:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0 	Yes	No		yes	no	One haplotype is missing from HiFi and Illumina reads in CBS because these reads align to an extra copy of the gene in GRCh38 (CBSL) that is not in HG002 (and CBSL is also not in GRCh37, T2T-CHM13, or most individuals)				skip																								44496062
Common		GRCh38			21	chr21	44496062	43075952	879	FN	C	G	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:100:tv:SNP:homalt	1/1:TP:gm:100:tv:SNP:homalt	CommonFN			yes	no	One haplotype is missing from HiFi and Illumina reads in CBS because these reads align to an extra copy of the gene in GRCh38 (CBSL) that is not in HG002 (and CBSL is also not in GRCh37, T2T-CHM13, or most individuals)													1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:TP:gm:30:tv:SNP:homalt	1/1:TP:gm:30:tv:SNP:homalt	1|1:TP:gm:12.4:tv:SNP:homalt	1/1:TP:gm:12.4:tv:SNP:homalt	1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:tv:SNP:homalt	.:.:.:0:.:NOCALL:nocall		44496062
Common		GRCh38			21	chr21	44496941	43076831	35	FN	C	T	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	One haplotype is missing from HiFi and Illumina reads in CBS because these reads align to an extra copy of the gene in GRCh38 (CBSL) that is not in HG002 (and CBSL is also not in GRCh37, T2T-CHM13, or most individuals)													0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:TP:gm:ti:SNP:het:30	0/1:TP:gm:ti:SNP:het:30	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0		44496941
DNAnexus	GRCh38_HG002_WGS_union.vcf.gz	GRCh38	small-variants	SNP	21	chr21	44496976	43076866	0	FP_FN	C	G	GT:BD:BK:QQ:BI:BVT:BLT	1|0:FN:am:.:tv:SNP:het	1/1:FP:am:0:tv:SNP:homalt 	yes	no		yes	no	One haplotype is missing from HiFi and Illumina reads in CBS because these reads align to an extra copy of the gene in GRCh38 (CBSL) that is not in HG002 (and CBSL is also not in GRCh37, T2T-CHM13, or most individuals)				skip																								44496976
Roche	RN_HG002_Illumina_PacBio_Oxford.vcf.gz	GRCh38	small-variants	SNP	21	chr21	44496976	43076866	0	FP_FN	C	G	GT:BD:BK:QQ:BI:BVT:BLT	1|0:FN:am:.:tv:SNP:het	1/1:FP:am:100:tv:SNP:homalt 	yes	no		yes	no	One haplotype is missing from HiFi and Illumina reads in CBS because these reads align to an extra copy of the gene in GRCh38 (CBSL) that is not in HG002 (and CBSL is also not in GRCh37, T2T-CHM13, or most individuals)				skip																								44496976
Common		GRCh38			21	chr21	44496976	43076866	92239	FP_FN	C	G	GT:BD:BK:QQ:BI:BVT:BLT	1|0:FN:am:.:tv:SNP:het	1/1:FP:am:100:tv:SNP:homalt	CommonFP_FN			yes	no	One haplotype is missing from HiFi and Illumina reads in CBS because these reads align to an extra copy of the gene in GRCh38 (CBSL) that is not in HG002 (and CBSL is also not in GRCh37, T2T-CHM13, or most individuals)													1|0:FN:.:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall	1|0:FN:am:.:tv:SNP:het	1/1:FP:am:796.77:tv:SNP:homalt	1|0:TP:gm:30:tv:SNP:het	0/1:TP:gm:30:tv:SNP:het	1|0:TP:gm:5.6:tv:SNP:het	0/1:TP:gm:5.6:tv:SNP:het	1|0:FN:am:.:tv:SNP:het	1/1:FP:am:0:tv:SNP:homalt	1|0:FN:am:.:tv:SNP:het	1/1:FP:am:39.33:tv:SNP:homalt	1|0:FN:am:.:tv:SNP:het	1/1:FP:am:35:tv:SNP:homalt		44496976
NYGC	HG-002-2x250-b38.recalibrated.haplotypeCalls.vcf.gz	GRCh38	small-variants	SNP	21	chr21	44589215	43169105	0	FN	C	T	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:.:ti:SNP:homalt:.	.:.:.:.:NOCALL:nocall:0 	unsure	unsure	Shallow coverage across technologies. Majority of ONT reads have Mapping Quality 0	yes	no	One haplotype is missing from HiFi and Illumina reads in CRYAA because these reads align to an extra copy of the gene in GRCh38 (CRYAA2) that is not in HG002 (and CRYAA2 is also not in GRCh37, T2T-CHM13, or most individuals). t also has a nearby 4kb repeat expansion plus a gap in the reference that causes low coverage even for ONT ultralong reads																												44589215
Common		GRCh38			21	chr21	44589215	43169105	354	FN	C	T	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:100:ti:SNP:homalt	1/1:TP:gm:100:ti:SNP:homalt	CommonFN			yes	no	One haplotype is missing from HiFi and Illumina reads in CRYAA because these reads align to an extra copy of the gene in GRCh38 (CRYAA2) that is not in HG002 (and CRYAA2 is also not in GRCh37, T2T-CHM13, or most individuals). t also has a nearby 4kb repeat expansion plus a gap in the reference that causes low coverage even for ONT ultralong reads													1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:TP:gm:30:ti:SNP:homalt	1/1:TP:gm:30:ti:SNP:homalt	1|1:TP:gm:5.2:ti:SNP:homalt	1/1:TP:gm:5.2:ti:SNP:homalt	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall		44589215
Roche	RN_HG002_Illumina_PacBio_Oxford.vcf.gz	GRCh38	small-variants	SNP	21	chr21	44589569	43169459	0	FN	C	T	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0 	yes	no		yes	no	One haplotype is missing from HiFi and Illumina reads in CRYAA because these reads align to an extra copy of the gene in GRCh38 (CRYAA2) that is not in HG002 (and CRYAA2 is also not in GRCh37, T2T-CHM13, or most individuals). t also has a nearby 4kb repeat expansion plus a gap in the reference that causes low coverage even for ONT ultralong reads				skip																								44589569
Common		GRCh38			21	chr21	44589569	43169459	351	FN	C	T	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	One haplotype is missing from HiFi and Illumina reads in CRYAA because these reads align to an extra copy of the gene in GRCh38 (CRYAA2) that is not in HG002 (and CRYAA2 is also not in GRCh37, T2T-CHM13, or most individuals). t also has a nearby 4kb repeat expansion plus a gap in the reference that causes low coverage even for ONT ultralong reads													0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:TP:gm:ti:SNP:het:30	0/1:TP:gm:ti:SNP:het:30	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0		44589569
DNAnexus	hs37d5_HG002_WGS_union.vcf.gz	GRCh37	small-variants	INDEL	21	chr21	44589920	43169810	139	FN	G	GC	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:.:i1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	yes	no		yes	no	One haplotype is missing from HiFi and Illumina reads in CRYAA because these reads align to an extra copy of the gene in GRCh38 (CRYAA2) that is not in HG002 (and CRYAA2 is also not in GRCh37, T2T-CHM13, or most individuals). t also has a nearby 4kb repeat expansion plus a gap in the reference that causes low coverage even for ONT ultralong reads																											21:44589920	43169810
Common		GRCh38			21	chr21	44590059	43169949	862	FN	C	T	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:29.2081:ti:SNP:homalt	1/1:TP:gm:29.2081:ti:SNP:homalt	CommonFN			yes	no	One haplotype is missing from HiFi and Illumina reads in CRYAA because these reads align to an extra copy of the gene in GRCh38 (CRYAA2) that is not in HG002 (and CRYAA2 is also not in GRCh37, T2T-CHM13, or most individuals). t also has a nearby 4kb repeat expansion plus a gap in the reference that causes low coverage even for ONT ultralong reads													1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:TP:gm:30:ti:SNP:homalt	1/1:TP:gm:30:ti:SNP:homalt	1|1:TP:gm:14.4:ti:SNP:homalt	1/1:TP:gm:14.4:ti:SNP:homalt	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:ti:SNP:homalt	.:.:.:0:.:NOCALL:nocall		44590059
Common		GRCh38			21	chr21	44590921	43170811	567	FN	G	A	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	One haplotype is missing from HiFi and Illumina reads in CRYAA because these reads align to an extra copy of the gene in GRCh38 (CRYAA2) that is not in HG002 (and CRYAA2 is also not in GRCh37, T2T-CHM13, or most individuals). t also has a nearby 4kb repeat expansion plus a gap in the reference that causes low coverage even for ONT ultralong reads													1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:ti:SNP:het:30	0/1:TP:gm:ti:SNP:het:30	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0		44590921
Common		GRCh38			21	chr21	44591488	43171378	129	FN	C	T	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	One haplotype is missing from HiFi and Illumina reads in CRYAA because these reads align to an extra copy of the gene in GRCh38 (CRYAA2) that is not in HG002 (and CRYAA2 is also not in GRCh37, T2T-CHM13, or most individuals). t also has a nearby 4kb repeat expansion plus a gap in the reference that causes low coverage even for ONT ultralong reads													1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:ti:SNP:het:30	0/1:TP:gm:ti:SNP:het:30	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0		44591488
Common		GRCh38			21	chr21	44591617	43171507	1258	FN	T	C	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	One haplotype is missing from HiFi and Illumina reads in CRYAA because these reads align to an extra copy of the gene in GRCh38 (CRYAA2) that is not in HG002 (and CRYAA2 is also not in GRCh37, T2T-CHM13, or most individuals). t also has a nearby 4kb repeat expansion plus a gap in the reference that causes low coverage even for ONT ultralong reads													1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:ti:SNP:het:30	0/1:TP:gm:ti:SNP:het:30	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0		44591617
Common		GRCh38			21	chr21	44592875	43172765	861567	FN	G	A	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	One haplotype is missing from HiFi and Illumina reads in CRYAA because these reads align to an extra copy of the gene in GRCh38 (CRYAA2) that is not in HG002 (and CRYAA2 is also not in GRCh37, T2T-CHM13, or most individuals). t also has a nearby 4kb repeat expansion plus a gap in the reference that causes low coverage even for ONT ultralong reads													1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:TP:gm:ti:SNP:het:30	0/1:TP:gm:ti:SNP:het:30	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:.:ti:SNP:het:.	.:.:.:.:NOCALL:nocall:0		44592875
Common		GRCh37			21	chr21	45454213	44034332	0	FN	A	AC	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			unsure	unsure	all techs are noisy in C homopolymer													0|1:TP:gm:i1_5:INDEL:het:169.73	0/1:TP:gm:i1_5:INDEL:het:169.73	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	21:45454213	44034332
Common		GRCh38			21	chr21	45454213	44034332	212366	FN	A	AC	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			unsure	unsure	all techs are noisy in C homopolymer													0|1:TP:gm:i1_5:INDEL:het:169.73	0/1:TP:gm:i1_5:INDEL:het:169.73	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0		45454213
Common		GRCh38			21	chr21	45666581	44246698	10996	FN	AC	A	GT:BD:BK:QQ:BI:BVT:BLT	1|1:TP:gm:100:d1_5:INDEL:homalt	1/1:TP:gm:100:d1_5:INDEL:homalt	CommonFN			yes	no	missed by short reads due to segdup													1|1:TP:gm:406.74:d1_5:INDEL:homalt	1/1:TP:gm:406.74:d1_5:INDEL:homalt	1|1:FN:.:.:d1_5:INDEL:homalt	.:.:.:0:.:NOCALL:nocall	1|1:TP:gm:30:d1_5:INDEL:homalt	1/1:TP:gm:30:d1_5:INDEL:homalt	1|1:FN:.:.:d1_5:INDEL:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:d1_5:INDEL:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:d1_5:INDEL:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:.:.:d1_5:INDEL:homalt	.:.:.:0:.:NOCALL:nocall		45666581
ITER	ITERteam_small-variation_GRCh37_ILMN-PB-ONT.vcf.gz	GRCh37	small-variants	SNP	21	chr21	45677577	44257694	1154065	FN	A	T	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:.:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	Unsure	Unsure	Only truth ILMN and query PacBio support this variant.	yes	no	illumina supports complex variants in adjacent homopolymer/TR, and other techs support but represent differently																											21:45677577	44257694
Common		GRCh37			21	chr21	46831674	45411759	7	FN	C	CGGGGGG	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:lm:i6_15:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			unsure	unsure	all techs noisy in G homopolymer													1|0:FN:lm:i6_15:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:lm:i6_15:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:lm:i6_15:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:lm:i6_15:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:lm:i6_15:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:lm:i6_15:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:lm:i6_15:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	21:46831674	45411759
Common		GRCh37			21	chr21	46831681	45411766	11	FN	T	G	GT:BD:BK:QQ:BI:BVT:BLT	1|0:TP:gm:10.0242:tv:SNP:het	0/1:TP:gm:10.0242:tv:SNP:het	CommonFN			unsure	unsure	all techs noisy in G homopolymer													1|0:FN:lm:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall	1|0:FN:lm:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall	1|0:FN:lm:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall	1|0:TP:gm:7.3:tv:SNP:het	0/1:TP:gm:7.3:tv:SNP:het	1|0:FN:lm:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall	1|0:FN:lm:.:tv:SNP:het	.:.:.:0:.:NOCALL:nocall	1|0:TP:gm:5:tv:SNP:het	0/1:TP:gm:5:tv:SNP:het	21:46831681	45411766
Common		GRCh37			21	chr21	46831692	45411777	78080	FN	C	G	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:lm:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			unsure	unsure	all techs noisy in G homopolymer													1|0:FN:lm:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:lm:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:lm:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:lm:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:lm:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:lm:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:lm:tv:SNP:het:.	.:.:.:.:NOCALL:nocall:0	21:46831692	45411777
ITER	ITERteam_small-variation_GRCh37_ILMN-PB-ONT.vcf.gz	GRCh37	small-variants	INDEL	21	chr21	46909771	45489857	99	FP_FN	CACTTGCCCCTCCCCCACACCTCCTCCCCG	C	GT:BD:BK:QQ:BI:BVT:BLT	0|1:FN:am:.:d16_plus:INDEL:het	1/1:FP:am:35.44:d16_plus:INDEL:homalt	Yes	No		yes	no	nearby dels in low complexity region that appear true though add up to >50bp																											21:46909771	45489857
Common		GRCh37			21	chr21	46909870	45489956	13014	FN	GCCCCACACCTCCTCCCCCACACCCTCCCCCACTTCCCCGTC	G	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:lm:d16_plus:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			yes	no	nearby dels in low complexity region that appear true though add up to >50bp													0|1:TP:gm:d16_plus:INDEL:het:319.73	0/1:TP:gm:d16_plus:INDEL:het:319.73	0|1:FN:.:d16_plus:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:d16_plus:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d16_plus:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d16_plus:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d16_plus:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:.:d16_plus:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	21:46909870	45489956
ITER	ITERteam_small-variation_GRCh37_ILMN-PB-ONT.vcf.gz	GRCh37	small-variants	INDEL	21	chr21	46922884	45502970	0	FN	CTAAGCAATTAAAAATGAAGTTTTAAAAAGGCA	C	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:lm:d16_plus:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	No	Yes	No support in both truth and query.	no	yes	likely hifiasm consensus error since no evidence in reads																											21:46922884	45502970
Common		GRCh37			21	chr21	46922884	45502970	0	FN	CTAAGCAATTAAAAATGAAGTTTTAAAAAGGCA	C	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:lm:d16_plus:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no	yes	likely hifiasm consensus error since no evidence in reads													0|1:FN:lm:d16_plus:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:d16_plus:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:d16_plus:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:d16_plus:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:d16_plus:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:d16_plus:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:d16_plus:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	21:46922884	45502970
Common		GRCh38			21	chr21	46922884	45502970	496393	FN	CTAAGCAATTAAAAATGAAGTTTTAAAAAGGCA	C	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:lm:d16_plus:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no	yes	likely hifiasm consensus error since no evidence in reads													0|1:FN:lm:d16_plus:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:d16_plus:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:d16_plus:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:d16_plus:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:d16_plus:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:d16_plus:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:d16_plus:INDEL:het:.	.:.:.:.:NOCALL:nocall:0		46922884
NCBI	HG002_grch37_dipcall.vcf.gz	GRCh37	small-variants	INDEL	21	chr21	47419277	45999363	-3351160	FP	G	GTT	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:lm:i1_5:INDEL:het	unsure	unsure	 benchmark for G/T; query for G/T or G/GTT;  evidence supoorts G/T het here	yes	no	all techs support benchmark																											21:47419277	45999363
DNAnexus	hs37d5_HG002_WGS_union.vcf.gz	GRCh37	small-variants	INDEL	22	chr22	43044209	42648203	55056	FP	TCCCCAAGGAGGAGACTCCAGGTCC	T	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:lm:d16_plus:INDEL:het	unsure	yes	Both the benchmark and the query callset called this deletion. This should not be a FP. Instead, this is just a difference in how to genotype format is presented.	yes	no	benchmark calls correct complex variant, and query is partially incorrect in region																											22:43044209	42648203
PacBio_gatk4	gatk4hc_HG002_15kb_20kb_52X_SequelII.vcf.gz	GRCh37	small-variants	INDEL	22	chr22	43099265	42703259	5789	FP_FN	G	GTTT,GTT	GT:BD:BK:QQ:BI:BVT:BLT	2|2:FN:lm:.:i1_5:INDEL:homalt	1/1:FP:lm:598.73:i1_5:INDEL:homalt	unsure	unsure	very difficult for human eyes to correctly assign genotype for 2T/3T multialleliics on a HP	yes	no	benchmark supported by all illumina reads crossing repeats																											22:43099265	42703259
Common		GRCh37			22	chr22	43105054	42709048	19	FN	A	ATATATATATAT	GT:BD:BK:BI:BVT:BLT:QQ	0|1:FN:lm:i6_15:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no	yes	benchmark has total of 17bp inserted instead of 20bp on one haplotype													0|1:FN:lm:i6_15:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:i6_15:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:i6_15:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:i6_15:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:i6_15:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:i6_15:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	0|1:FN:lm:i6_15:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	22:43105054	42709048
Common		GRCh37			22	chr22	43105073	42709067	5977	FP_FN	A	ATATATATATTTTTT,ATTTTTT,ATATATATATATATTTTTTTT	GT:BD:BK:BI:QQ:BVT:BLT	1|2:FN:am:i6_15:.:INDEL:hetalt	3/1:FP:am:i16_plus,i6_15:100:INDEL:hetalt	CommonFP_FN			no	yes	benchmark has total of 17bp inserted instead of 20bp on one haplotype													1|2:FN:am:i6_15:.:INDEL:hetalt	3/1:FP:am:i16_plus,i6_15:1574.73:INDEL:hetalt	1|2:FN:am:i6_15:.:INDEL:hetalt	3/1:FP:am:i16_plus,i6_15:581.73:INDEL:hetalt	1|2:FN:am:i6_15:.:INDEL:hetalt	3/1:FP:am:i16_plus,i6_15:30:INDEL:hetalt	1|2:FN:am:i6_15:.:INDEL:hetalt	3/1:FP:am:i16_plus,i6_15:708.1:INDEL:hetalt	1|2:FN:am:i6_15:.:INDEL:hetalt	1/1:FP:am:i6_15:0:INDEL:homalt	1|2:FN:am:i6_15:.:INDEL:hetalt	3/1:FP:am:i16_plus,i6_15:202.12:INDEL:hetalt	1|2:FN:am:i6_15:.:INDEL:hetalt	1/1:FP:am:i6_15:8:INDEL:homalt	22:43105073	42709067
Common		GRCh37			22	chr22	43111050	42715044	0	FP	T	TG	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:.:i1_5:INDEL:het	CommonFP			no	yes	hifiasm misses haplotype in homopolymer due to highly homozygous region													.:.:.:.:.:NOCALL:nocall	0/1:351.73:FP:.:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:249.73:FP:.:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:.:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:313.64:FP:.:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:.:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:50:FP:.:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:10:FP:.:i1_5:INDEL:het	22:43111050	42715044
Common		GRCh38			22	chr22	43111050	42715044	326488	FP	T	TG	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:.:i1_5:INDEL:het	CommonFP			no	yes	hifiasm misses haplotype in homopolymer due to highly homozygous region													.:.:.:.:.:NOCALL:nocall	0/1:351.73:FP:.:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:249.73:FP:.:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:.:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:152.64:FP:.:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:0:FP:.:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:50:FP:.:i1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:10:FP:.:i1_5:INDEL:het		43111050
NYGC	HG-002-2x250-b38.recalibrated.haplotypeCalls.vcf.gz	GRCh38	small-variants	INDEL	22	chr22	43437538	43041532	27859	FP_FN	C	CTTTTTTT,CTTTTTTTTT	GT:BD:BK:BI:QQ:BVT:BLT	2|1:FN:am:i6_15:.:INDEL:hetalt	1/1:FP:am:i6_15:661.73:INDEL:homalt 	yes	yes		yes	no	almost all of the illumina reads that cross the homopolymer support the 9bp and 7bp insertions, and the average of each HiFi haplotype supports this, so benchmark is likely correct despite long homopolymer																												43437538
Common		GRCh37			22	chr22	43465397	43069391	0	FP_FN	C	CA	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:100:i1_5:INDEL:het	CommonFP_FN			no	yes	hifiasm misses haplotype in homopolymer due to noisy HiFi and/or slightly homozygous region													1|1:FN:.:.:i1_5:INDEL:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:48.77:i1_5:INDEL:het	1|1:TP:gm:30:i1_5:INDEL:homalt	1/1:TP:gm:30:i1_5:INDEL:homalt	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:42.69:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:0:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:27.31:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:8:i1_5:INDEL:het	22:43465397	43069391
Common		GRCh38			22	chr22	43465397	43069391	3934	FP_FN	C	CA	GT:BD:BK:QQ:BI:BVT:BLT	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:100:i1_5:INDEL:het	CommonFP_FN			no	yes	hifiasm misses haplotype in homopolymer due to noisy HiFi and/or slightly homozygous region													1|1:FN:.:.:i1_5:INDEL:homalt	.:.:.:0:.:NOCALL:nocall	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:59.77:i1_5:INDEL:het	1|1:TP:gm:30:i1_5:INDEL:homalt	1/1:TP:gm:30:i1_5:INDEL:homalt	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:73.64:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:0:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:27.62:i1_5:INDEL:het	1|1:FN:am:.:i1_5:INDEL:homalt	0/1:FP:am:8:i1_5:INDEL:het		43465397
BCM-HGSC_xAtlas	HG002.GRCh38.60x.1_merged.vcf.gz	GRCh38	small-variants	INDEL	22	chr22	43469331	43073325	504	FP	CTATT	C	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:7:FP:am:d1_5:INDEL:het 	Yes	No		yes	no	callset misses larger del				skip																								43469331
Common		GRCh37			22	chr22	43469835	43073829	598	FN	A	AT	GT:BD:BK:BI:BVT:BLT:QQ	1|0:FN:lm:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no	yes	hifiasm error due to noisy in homopolymer													1|0:FN:lm:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:lm:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:lm:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:lm:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:lm:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:lm:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	1|0:FN:lm:i1_5:INDEL:het:.	.:.:.:.:NOCALL:nocall:0	22:43469835	43073829
BCM-HGSC_xAtlas	HG002.hs37d5.60x.1_merged.vcf.gz	GRCh37	small-variants	INDEL	22	chr22	43470433	43074427	0	FN	CA	C	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:lm:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0 	Yes	No		no	yes	hifiasm misses haplotype in homopolymer due to noisy HiFi and/or slightly homozygous region																											22:43470433	43074427
Common		GRCh37			22	chr22	43470433	43074427	0	FP	CAA	C	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:lm:d1_5:INDEL:het	CommonFP			no	yes	hifiasm misses haplotype in homopolymer due to noisy HiFi and/or slightly homozygous region													./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:594.06:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	1/1:0:FP:lm:d1_5:INDEL:homalt	.:.:.:.:.:NOCALL:nocall	0/1:158.16:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:5:FP:lm:d1_5:INDEL:het	22:43470433	43074427
Common		GRCh37			22	chr22	43470433	43074427	0	FN	CA	C	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:am:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no	yes	hifiasm misses haplotype in homopolymer due to noisy HiFi and/or slightly homozygous region													1|1:TP:gm:d1_5:INDEL:homalt:164.73	1/1:TP:gm:d1_5:INDEL:homalt:164.73	1|1:TP:gm:d1_5:INDEL:homalt:243.73	1/1:TP:gm:d1_5:INDEL:homalt:243.73	1|1:FN:am:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:am:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:d1_5:INDEL:homalt:0	.:.:.:.:NOCALL:nocall:0	1|1:FN:am:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:lm:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	22:43470433	43074427
Common		GRCh38			22	chr22	43470433	43074427	0	FN	CA	C	GT:BD:BK:BI:BVT:BLT:QQ	1|1:FN:am:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	CommonFN			no	yes	hifiasm misses haplotype in homopolymer due to noisy HiFi and/or slightly homozygous region													1|1:TP:gm:d1_5:INDEL:homalt:164.73	1/1:TP:gm:d1_5:INDEL:homalt:164.73	1|1:TP:gm:d1_5:INDEL:homalt:337.73	1/1:TP:gm:d1_5:INDEL:homalt:337.73	1|1:FN:am:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:am:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:TP:gm:d1_5:INDEL:homalt:0	.:.:.:.:NOCALL:nocall:0	1|1:FN:am:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0	1|1:FN:lm:d1_5:INDEL:homalt:.	.:.:.:.:NOCALL:nocall:0		43470433
Common		GRCh38			22	chr22	43470433	43074427	13410	FP	CAA	C	GT:QQ:BD:BK:BI:BVT:BLT	.:.:.:.:.:NOCALL:nocall	0/1:100:FP:lm:d1_5:INDEL:het	CommonFP			no	yes	hifiasm misses haplotype in homopolymer due to noisy HiFi and/or slightly homozygous region													./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	./.:.:.:.:.:.:.	.:.:.:.:.:NOCALL:nocall	0/1:30:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:387.06:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	1/1:0:FP:lm:d1_5:INDEL:homalt	.:.:.:.:.:NOCALL:nocall	0/1:158.08:FP:lm:d1_5:INDEL:het	.:.:.:.:.:NOCALL:nocall	0/1:5:FP:lm:d1_5:INDEL:het		43470433
NCBI	HG002_grch37_dipcall.vcf.gz	GRCh37	small-variants	INDEL	22	chr22	43483843	43087837	-43087837	FP_FN	C	CAA,CA	GT:BD:BK:BI:QQ:BVT:BLT	1|2:FN:am:i1_5:.:INDEL:hetalt	1/1:FP:am:i1_5:30:INDEL:homalt	unsure	unsure	evidence for 1A-3A INS here; repeat region	yes	no	benchmark supported by illumina reads that cross repeat																											22:43483843	43087837