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.
High Depth and GQ of 0
I am attempting to get an "expected quality (GQ)" given a certain depth of coverage in a VCF file in order to quantify a rough minimum depth that will result in a usable variant call, and I noticed some odd behavior. In one of my variants, I have a depth of 601 (all referent), but the GQ is reported as 0. For a SNP, the PL is typically reported as "0,0,1000+". Below is a sample of the issue at 16:55862791 (note that the filter applied here is GQ>50):
GVCF entry: ... T . . END=55862791 GT:DP:GQ:MIN_DP:PL 0/0:601:0:601:0,0,13743
For the record, I am using the HaplotypeCaller version 3.2-0 (calling GVCFs). If you need anything else from me to help diagnose the issue, please let me know.