Scripts for benchmark

# K-mer method
#!/bin/sh
perl sort_uniq.pl DRR054198
perl count.pl DRR054198
perl snp.pl DRR054198 IRGSP1.0
perl map.pl DRR054198 IRGSP1.0
perl verify_snp.pl DRR054198 default IRGSP1.0 AAA kmer
perl snp2vcf.pl DRR054198 kmer

#!/bin/sh
perl sort_uniq.pl ERR3063487
perl count.pl ERR3063487
perl snp.pl ERR3063487 WBcel235
perl map.pl ERR3063487 WBcel235
perl verify_snp.pl ERR3063487 default WBcel235 AAA kmer
perl snp2vcf.pl ERR3063487 kmer

# Bidirectional alignment method
#!/bin/sh
perl sort_uniq.pl DRR054198
perl align.pl DRR054198 IRGSP1.0 5
perl split_snp.pl DRR054198
perl verify_snp.pl DRR054198 default IRGSP1.0 01 bi
perl snp2vcf.pl DRR054198

#!/bin/sh
perl sort_uniq.pl ERR3063487
perl align.pl ERR3063487 WBcel235 5
perl split_snp.pl ERR3063487 WBcel235
perl verify_snp.pl ERR3063487 default WBcel235 01 bi
perl snp2vcf.pl ERR3063487

# Pipeline of bwa, Samtools and GATK
#!/bin/sh
bwa mem IRGSP1.0.fa DRR003659/read/DRR003659_1.fastq DRR003659/read/DRR003659_2.fastq > DRR003659.sam
samtools view -bS DRR003659.sam > DRR003659.bam
samtools sort DRR003659.bam > DRR003659_sorted.bam
java -jar picard.jar AddOrReplaceReadGroups I=DRR003659_sorted.bam O=DRR003659_sorted_header.bam RGID=4 RGLB=lib1 RGPL=illumina RGPU=unit1 RGSM=DRR003659 VALIDATION_STRINGENCY=SILENT
samtools index DRR003659_sorted_header.bam
./gatk HaplotypeCaller -R IRGSP1.0.fa -I DRR003659_sorted_header.bam --output DRR003659_gatk4.0.vcf

#!/bin/sh
bwa mem Caenorhabditis_elegans.WBcel235.dna.toplevel read/ERR3063487_1.fastq read/ERR3063487_2.fastq > ERR3063487.sam
samtools view -bS ERR3063487.sam > ERR3063487.bam
samtools sort ERR3063487.bam > ERR3063487_sorted.bam
samtools faidx Caenorhabditis_elegans.WBcel235.dna.toplevel.fa
java -jar picard.jar CreateSequenceDictionary R=Caenorhabditis_elegans.WBcel235.dna.toplevel.fa O=Caenorhabditis_elegans.WBcel235.dna.toplevel.dict
java -jar ./picard.jar AddOrReplaceReadGroups I=ERR3063487_sorted.bam O=ERR3063487_sorted_header.bam RGID=4 RGLB=lib1 RGPL=illumina RGPU=unit1 RGSM=ERR3063487 VALIDATION_STRINGENCY=SILENT
samtools index ERR3063487_sorted_header.bam
./gatk HaplotypeCaller -R Caenorhabditis_elegans.WBcel235.dna.toplevel.fa -I ERR3063487_sorted_header.bam --output ERR3063487_gatk4.0.vcf