Hi, I have been trying to manually filter a vcf file by QD score, but I have not been able to do it properly. I thought of using awk and indicate that a specific field has a value greater than 8 (that is the value I want to filter it), but I have records where the QD variable does not occupy the same position.
1 2422614 . G A 3711.77 . AF=1;DP=120;ExcessHet=3.0103;FS=0;MLEAC=2;MLEAF=1;MQ=60;QD=30.93;SOR=1.773 GT:AD:ADO:DP:GQ:PL 1/1:0,120:0:120:99:0 1 2430617 . C T 2052.76 . AF=0.5;BaseQRankSum=-1.791;ClippingRankSum=0;DP=292;ExcessHet=3.0103;FS=6.978;MLEAC=1;MLEAF=0.5;MQ=60;MQRankSum=0;QD=7.03;ReadPosRankSum=-1.813;SOR=0.652 GT:AD:ADO:DP:GQ:PL 0/1:144,148:0:292:99:3740
Thank you very much