I am trying to manually filter the results from HaplotypeCaller because my organism is anything but model. I sequenced 60 samples and had an average coverage of ~60X per sample across the genome.
As shown in an excerpt from my HaplotypeCaller output below, "DP=3201". Is this the total depth? i.e. across 60 samples the average is 53.35? This number makes sense. If this is the case, is there any way to exclude SNPs in which ANY INDIVIDUAL sample has a depth of less than 20? As opposed to an average depth of less than 20.
I've been using SelectVariants as such:
java -jar /home/berrya/bin/GenomeAnalysisTK.jar -T SelectVariants -R /path/to/reference.fasta -V HaplotypeCaller_output.vcf -select "DP >=20" -select "QUAL > 30.0" -select "QD < 2.0 || FS > 60.0 || SOR > 4.0 || MQ < 40.0 || MQRankSum < -12.5 ||ReadPosRankSum < -8.0" -o output.vcf
When I raise the DP variable to "DP >=1000", no additional SNPs are cut, which is how I know it's not doing what I'm expecting it to be doing.
I appreciate any guidance.
Alex
KB223232.1 200 . T A 112397.32 .
AC=120;AF=1.00;AN=120;BaseQRankSum=1.50;ClippingRankSum=0.945;DP=3201;ExcessHet=3.0103;FS=0.000;InbreedingCoeff=-0.0000;MLEAC=120;MLEAF=1.00;MQ=36.90;MQRankSum=0.394;QD=34.24;ReadPosRankSum=-1.339e+00;SOR=0.223 GT:AD:DP:GQ:PL 1/1:0,53:53:99:1865,159,0 1/1:0,47:47:99:1744,141,0 1/1:0,179:179:99:6518,536,0 1/1:0,40:40:99:1432,119,0 1/1:0,15:15:45:497,45,0 1/1:0,20:20:59:679,59,0 1/1:0,39:39:99:1317,116,0 1/1:0,63:63:99:2167,187,0 1/1:0,34:34:99:1274,102,0 1/1:0,30:30:90:1105,90,0 1/1:1,43:44:99:1507,121,0 1/1:0,140:140:99:5024,418,0 1/1:0,17:17:50:558,50,0 1/1:0,39:39:99:1315,116,0 1/1:0,24:24:72:872,72,0 1/1:0,17:17:50:534,50,0 1/1:0,34:34:99:1158,101,0 1/1:0,33:33:97:1053,97,0 1/1:0,36:36:99:1133,106,0 1/1:0,71:71:99:2572,212,0 1/1:0,35:35:99:1220,104,0 1/1:0,42:42:99:1512,126,0 1/1:0,39:39:99:1402,116,0 1/1:0,44:44:99:1602,131,0 1/1:0,42:42:99:1419,124,0 1/1:0,126:126:99:4695,378,0 1/1:0,48:48:99:1708,143,0 1/1:0,41:41:99:1487,123,0 1/1:0,132:132:99:4789,396,0 1/1:0,39:39:99:1340,116,0 1/1:0,131:131:99:4785,393,0 1/1:0,34:34:99:1161,101,0 1/1:0,35:35:99:1304,105,0 1/1:0,27:27:81:1001,81,0 1/1:0,32:32:96:1190,96,0 1/1:0,51:51:99:1840,153,0 1/1:0,38:38:99:1347,114,0 1/1:0,64:64:99:2151,190,0 1/1:0,47:47:99:1684,140,0 1/1:0,66:66:99:2346,197,0 1/1:0,64:64:99:2210,190,0 1/1:0,51:51:99:1846,153,0 1/1:0,48:48:99:1651,142,0 1/1:0,20:20:60:744,60,0 1/1:0,38:38:99:1369,114,0 1/1:0,20:20:59:691,59,0 1/1:0,65:65:99:2307,193,0 1/1:0,181:181:99:6516,542,0 1/1:0,60:60:99:2022,177,0 1/1:0,44:44:99:1586,131,0 1/1:0,133:133:99:4473,394,0 1/1:0,44:44:99:1527,131,0 1/1:0,42:42:99:1369,124,0 1/1:0,51:51:99:1794,152,0 1/1:0,38:38:99:1321,113,0 1/1:0,85:85:99:2941,255,0 1/1:0,42:42:99:1299,122,0 1/1:0,28:28:83:957,83,0 1/1:0,26:26:76:856,76,0