QD scores smaller than expected for indel calls
According to the definition of QD, it equals to the variant confidence (from the QUAL field) divided by the unfiltered depth of non-reference samples.
However, when I ran the Unified Genotyper (v2.8.1) on a pair of samples for indel calls, the QD score for some indels are much lower than expected. For example,
chrX 51075762 . GCAGCTGCGT G 142.15 . AC=1;AF=0.250;AN=4;BaseCounts=0,0,204,0;BaseQRankSum=-1.435;DP=204;FS=0.000;GC=70.82;LowMQ=0.0049,0.0049,204;MLEAC=1;MLEAF=0.250;MQ=55.32;MQ0=0;MQRankSum=-2.698;QD=0.15;ReadPosRankSum=-3.784;Samples=tumor_DNA_2C;VariantType=DELETION.NumRepetitions_1.EventLength_9 GT:AD:DP:GQ:PL 0/0:94,0:95:99:0,283,11503 0/1:101,7:108:99:181,0,11532
in this case, the expected QD = 142.15 / 108 = 1.32, but the reported QD = 0.15
chr21 45649571 . C CCTGGACCCGCCCTGGACACCCCACGGGGG 526.15 . AC=1;AF=0.250;AN=4;BaseCounts=0,78,0,0;BaseQRankSum=0.787;DP=78;FS=0.000;GC=65.84;LowMQ=0.0000,0.0000,78;MLEAC=1;MLEAF=0.250;MQ=60.33;MQ0=0;MQRankSum=1.453;QD=0.44;ReadPosRankSum=-3.875;Samples=tumor_DNA_2C;VariantType=INSERTION.NOVEL_10orMore GT:AD:DP:GQ:PL 0/0:31,1:37:86:0,86,3672 0/1:30,6:41:99:565,0,4204
the expected QD = 526.15 / 41 = 12.83, the reported QD 0.44 is much smaller.
Do you know what's happening? Should I filter those indel calls (since QD < 2.0)?