Hi, I have raw calls for indels called using GATK, I wonder, where to start? filtering these calls? Should I plot the quality, depth etc. and then decide threshold to filter the bad calls? Any suggestions, scripts would be useful.
chr10 264423 . G GC 29875 . AC=26;AF=1.00;AN=26;BaseQRankSum=-0.054;DP=717;FS=8.633;HaplotypeScore=344.1280;InbreedingCoeff=-0.0046;MLEAC=26;MLEAF=1.00;MQ=38.57;MQ0=0;MQRankSum=-0.832;QD=41.67;RPA=1,2;RU=C;ReadPosRankSum=0.979;SB=-4.035e+03;STR GT:AD:DP:GQ:PL 1/1:6,242:250:99:10448,743,0 1/1:10,193:203:99:8479,571,0 1/1:3,142:148:99:6167,439,0 1/1:0,13:13:39:551,39,0 1/1:1,9:10:30:424,30,0 1/1:1,13:15:39:550,39,0 1/1:0,9:9:27:382,27,0 1/1:1,15:16:48:667,48,0 1/1:1,11:12:33:467,33,0 1/1:1,8:9:27:382,27,0 1/1:0,18:18:54:764,54,0 1/1:0,11:11:33:467,33,0 1/1:0,3:3:9:127,9,0
Looking forward for your suggestions and feedback. /Bari,