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How read depth is calculated?

AswathyNAswathyN BangaloreMember

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?


Best Answer


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