I am using GATK 3.5 to call SNPs/indels. For some variants, the DP argument is ".", but the GQ is not ".". For example in the second sample below, the "1/1" genotype is called with a depth of zero and a high confidence.
chr1 13859273 . C T 21107.89 . AC=18;AF=0.818;AN=22;BaseQRankSum=1.113;ClippingRankSum=0.429;DP=398;FS=0.000;InbreedingCoeff=0.9591;MQ=60.00;MQ0=0;MQRankSum=-0.139;QD=35.55;ReadPosRankSum=5.678;SOR=3.213 GT:AD:DP:GQ:PL 1/1:0,28:28:84:1260,84,0 1/1:.:.:99:2004,138,0
Does anyone know how this is possible? Thk.