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0/0 genotypes in GenotypeGVCFs
I want to call both confident variants and confident homREF genotypes using gatk 3.x style (pretty much like EMIT_ALL_CONFIDENT_SITES in UnifiedGenotyper). I first use HaplotypeCaller with -ERC GVCF, then use GenotypeGVCFs -inv to emit all confident sites. However, in the resulting vcf file, there is no site with a 0/0 genotype for all samples in the jointly called vcf, which contains only variant sites and sites with ./. genotype for all samples. I do think all sites are in the vcf file. Why can't I find any site with 0/0 genotype for all samples in the vcf from GenotypeGVCFs? Or do I need to run HaplotypeCaller with -ERC BP_RESOLUTION first? Thanks!