## Supplementary file 1 
# HaplotypeCaller command used for each sample :

java –Xmx16g –jar GenomeAnalysisTK.jar –T HaplotypeCaller –R UMD3.1.fa –I sample.bam –nct 4 –variant_index_type LINEAR – variant_index_parameter 128000 –emitRefConfidence GVCF –o raw.snps.indels.g.vcf.