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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?