Hi,
I follow this thread to execute results from a trio but I discover there are many duplicate records after CalculateGenotypePosteriors.
Code brief describe here:
java -Xmx16g -jar gatk-package-4.0.0.0-local.jar CalculateGenotypePosteriors -R Homo_sapiens_assembly38.fasta -ped trio.ped -supporting 1000G.phase3.integrated.sites_only.no_MATCHED_REV.hg38.vcf.gz -V trio.recal.vcf.gz -O trio.recal.refine.vcf.gz
I also discover the output is not gz format, just vcf.
Recalibrated variants (part)
chr1 3872413 . AG A 400.09 PASS AC=1;AF=0.167;AN=6;BaseQRankSum=-4.760e-01;ClippingRankSum=0.00;DP=110;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.167;MQ=60.00;MQRankSum=0.00;QD=10.53;ReadPosRankSum=-1.513e+00;SOR=0.787;VQSLOD=4.73;culprit=ReadPosRankSum GT:AD:DP:GQ:PL 0/0:27,0:27:81:0,81,712 0/0:45,0:45:99:0,111,1665 0/1:17,21:38:99:440,0,469
chr1 3872414 . GA G 29.18 PASS AC=1;AF=0.167;AN=6;BaseQRankSum=0.246;ClippingRankSum=0.00;DP=126;ExcessHet=3.0103;FS=1.192;MLEAC=1;MLEAF=0.167;MQ=76.93;MQRankSum=0.00;QD=0.50;ReadPosRankSum=0.352;SOR=0.472;VQSLOD=3.93;culprit=QD GT:AD:DP:GQ:PL 0/0:29,0:29:16:0,16,666 0/1:48,10:58:69:69,0,1051 0/0:35,3:38:54:0,54,912
chr1 3883678 . A G 2352.16 PASS AC=2;AF=0.333;AN=6;BaseQRankSum=1.48;ClippingRankSum=0.00;DP=311;ExcessHet=3.9794;FS=1.518;MLEAC=2;MLEAF=0.333;MQ=60.00;MQRankSum=0.00;POSITIVE_TRAIN_SITE;QD=9.33;ReadPosRankSum=-1.164e+00;SOR=0.709;VQSLOD=23.18;culprit=MQ GT:AD:DP:GQ:PL 0/0:59,0:59:99:0,120,1800 0/1:69,51:120:99:964,0,1565 0/1:65,67:132:99:1420,0,1292
After CalculateGenotypePosteriors (part)
chr1 3872413 . AG A 400.09 PASS AC=1;AF=0.167;AN=6;BaseQRankSum=-4.760e-01;ClippingRankSum=0.00;DP=110;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.167;MQ=60.00;MQRankSum=0.00;PG=0,0,0;QD=10.53;ReadPosRankSum=-1.513e+00;SOR=0.787;VQSLOD=4.73;culprit=ReadPosRankSum GT:AD:DP:GQ:JL:JP:PL:PP 0/0:27,0:27:81:80:80:0,81,712:0,81,772 0/0:45,0:45:99:80:80:0,111,1665:0,111,1725 0/1:17,21:38:99:80:80:440,0,469:440,0,529
chr1 3872414 . GA G 29.18 PASS AC=1;AF=0.167;AN=6;BaseQRankSum=0.246;ClippingRankSum=0.00;DP=126;ExcessHet=3.0103;FS=1.192;MLEAC=1;MLEAF=0.167;MQ=76.93;MQRankSum=0.00;PG=0,0,0;QD=0.50;ReadPosRankSum=0.352;SOR=0.472;VQSLOD=3.93;culprit=QD GT:AD:DP:GQ:JL:JP:PL:PP 0/0:29,0:29:16:16:16:0,16,666:0,16,719 0/1:48,10:58:69:16:16:69,0,1051:69,0,1067 0/0:35,3:38:54:16:16:0,54,912:0,54,928
chr1 3872413 . AG A 400.09 PASS AC=1;AF=0.167;AN=6;BaseQRankSum=-4.760e-01;ClippingRankSum=0.00;DP=110;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.167;MQ=60.00;MQRankSum=0.00;PG=0,0,0;QD=10.53;ReadPosRankSum=-1.513e+00;SOR=0.787;VQSLOD=4.73;culprit=ReadPosRankSum GT:AD:DP:GQ:JL:JP:PL:PP 0/0:27,0:27:81:80:80:0,81,712:0,81,772 0/0:45,0:45:99:80:80:0,111,1665:0,111,1725 0/1:17,21:38:99:80:80:440,0,469:440,0,529
chr1 3872414 . GA G 29.18 PASS AC=1;AF=0.167;AN=6;BaseQRankSum=0.246;ClippingRankSum=0.00;DP=126;ExcessHet=3.0103;FS=1.192;MLEAC=1;MLEAF=0.167;MQ=76.93;MQRankSum=0.00;PG=0,0,0;QD=0.50;ReadPosRankSum=0.352;SOR=0.472;VQSLOD=3.93;culprit=QD GT:AD:DP:GQ:JL:JP:PL:PP 0/0:29,0:29:16:16:16:0,16,666:0,16,719 0/1:48,10:58:69:16:16:69,0,1051:69,0,1067 0/0:35,3:38:54:16:16:0,54,912:0,54,928
chr1 3883678 . A G 2352.16 PASS AC=2;AF=0.333;AN=6;BaseQRankSum=1.48;ClippingRankSum=0.00;DP=311;ExcessHet=3.9794;FS=1.518;MLEAC=2;MLEAF=0.333;MQ=60.00;MQRankSum=0.00;PG=0,0,6;POSITIVE_TRAIN_SITE;QD=9.33;ReadPosRankSum=-1.164e+00;SOR=0.709;VQSLOD=23.18;culprit=MQ GT:AD:DP:GQ:JL:JP:PL:PP 0/0:59,0:59:99:119:119:0,120,1800:0,120,1805 0/1:69,51:120:99:119:119:964,0,1565:964,0,1631 0/1:65,67:132:99:119:119:1420,0,1292:1420,0,1358