Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
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!