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.
How read depth is calculated?
12 112037109 . A AGTC 31.17 PASS AC=1;AF=0.042;AN=2;BaseQRankSum=-2.034e+00;ClippingRankSum=-5.550e-01;DP=139;FS=3.090;GQ_MEAN=8.42;GQ_STDDEV=16.54;InbreedingCoeff=-0.2414;MLEAC=2;MLEAF=0.083;MQ=34.42;MQ0=0;MQRankSum=-5.550e-01;NCC=25;QD=2.60;ReadPosRankSum=-7.510e-01;VQSLOD=-6.959e-01;culprit=QD GT:AD:DP:GQ:PL 0/1:9,3:12:59:59,0,793
In my Targetted Exome sample for variant calling, I notice that the read depth (DP) in the GT field is much less (ie. 12) compared to DP field in the INFO column (ie. 139). I would like to know,
1. What is the relation between read depth in both the fields?
2. How is the read depth calculated in both the cases?