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.
Genotypes in vcf with a GQ=0
I'm using GATK version 3.7 and I have a problem similar to the point raised in 2015 and titled "Unexpected genotype likelihoods & genotype qualities".
I've used HaplotypeCaller to generate individual GVCFs and after that, have used GenotypeGVCFs on multiple individual samples.
In the resulting vcf, I have some genotypes 0/0 with a GQ=0, whereas I was waiting for genotypes ./. (I suppose that when 2 genotypes have the same probability, the genotype should be unknown).
Could you please tell me how to do to force GATK to put ./. when GQ=0 ?
I've tried the GenotypeGVCFs command with teh version 3.8 and there's the same problem.
Thank very much.