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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