Dear GATK community,
We have been using GATK tools for many years and are quite happy with them. We generally use two types of calls.
1) Variant calls for the more or less usual clinical reasons, and
2) GWAS style calls where we emit all calls for a specific set of alleles, usually along the 1000 genome project, generally something like the following, plus some java flags and other flags dictated by the HPC system we are running them on:
I am trying to both reduce the computational cost and the number of times I have to move hundreds of genomes in and out of storage into the HPC system by calling genomes using gvcf files and extracting the calls I need from there. Extracting a vcf variant file from a gvcf is relatively straightforward using GenotypeGVCFs , but I can't find a way to coax a call of the type 2) above out of any of your canonical tools. Does anyone have suggestions about how to do that? Thanks a lot,
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