High Depth and GQ of 0

johnwallace123johnwallace123 Member ✭✭
edited October 2014 in Ask the GATK team

GATK Gurus,

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):

Entry: 0/0:.:601,0:601:LowQualCall:0:0,0,13743
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.

-John Wallace

Post edited by Geraldine_VdAuwera on

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