I am hoping to perform hard filtering on some variants from a sequencing project where, unfortunately, I do not have information from enough samples for VQSR. I was planning to filter on the QD value, but it seems to be very low for variants that seem reasonable. Example:
chr7 55249063 . G A 225 PASS AC=1;AC1=1;AF=0.500;AF1=0.5;AN=2;BaseQRankSum=1.307;DP=4582;DP4=937,935,1299,1316;Dels=0.00;FQ=225;FS=0.323; HaplotypeScore=390.2899;MQ=59.95;MQ0=0;MQRankSum=-1.910;PV4=0.81,1,1,1;QD=0.05;ReadPosRankSum=4.848;VDB=0.0003 GT:AD:GQ:PL 0/1:1917,2657:99:255,0,255
This variant is shown in IGV in the attached file- it looks to be a true positive, but because of the high depth, QD is very low. Based on the QD documentation, it looks as QD simply cannot be used to filter high-coverage data, since the value is QUAL/unfiltered depth.
Is there an alternative annotation that expresses the same measure, since QD is recommended in all the hard filtering documentation? Would GQ be a good substitute?
Your help is much appreciated!