We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!
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.
True read depth in VCF files
I'm trying to filter my prospective variants based on read depth in each of the samples, but the VCF file produced by HaplotypeCaller doesn't appear to have the true depth in each sample recorded anywhere. I'm running HaplotypeCaller without downsampling, and neither the Format DP or the Format AD fields seem to be reflecting true depth in the sample. One example of the output (including only one sample for simplicity) is:
gi|704001763|gb|KM360047.1| TRUE TRUE 41767 . A "G,T" 724766.51 . "AC=18,1;AF=0.947,0.053;AN=19;BaseQRankSum=1.459;ClippingRankSum=-1.426;DP=16148;FS=0.000;MLEAC=18,1;MLEAF=0.947,0.053;MQ=47.70;MQRankSum=1.505;QD=30.05;ReadPosRankSum=1.533;SOR=1.438" GT:AD:DP:GQ:PL "1:0,298,0:298:99:13341,0,11125"
The true depth at this position in the sample (as determined by examination of the raw reads in IGV) is 1002, and the total depth for all samples should be over 17000.
Any idea where (if anywhere) I can find true read depth in the VCF file, or do I have to calculate that separately?