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# from: Mahyar

BostonMember

I run UnifiedGenotyper for my 42 samples (bam files) to get VCF file. after almost 48 hours I got my vcf file but there was no 0/0 reference homozygous genotype in the vcf file. How I can achieve these genotype information? I need them for the eQTL analyses. I want to see all 3 class of genotype in the vcf file (0/0, 0/1, and 1/1). Thanks

Tagged:

• Member

So after the column 'GT:AD:DP:GQ:PL' you have no columns with 0/0 in them?, what do you have?, ./. or 0/1 or 1/1?

• BostonMember

Problem in VCF file:
More than 80% of SNP sites in my VCF file are "./." after calling variants using UnifiedGenotyper!
Is it normal or there is something wrong for unifiedgenotyper procedure or BAM files or something else? Please advise. Thanks