Hi GATK team,
I found some abnormal output lines in VCF file which was generated by HaplotypeCaller in GATK 2.2.5 pipeline, with default parameters:
0/2 genotype reported for a bi-allelic loci:
SCF35 934292 . T G 52146.48 . AC=60;AF=0.909;AN=66;ActiveRegionSize=272;BaseQRankSum=5.365;ClippingRankSum=0.827;DP=403;EVENTLENGTH=0;FS=1.133;HaplotypeScore=31.6690;InbreedingCoeff=-0.1000;MLEAC=60;MLEAF=0.909;MQ=91.89;MQ0=0;MQRankSum=-1.672;NVH=5;NumHapAssembly=4;NumHapEval=4;QD=129.40;QDE=25.88;ReadPosRank8,9,148,148 0/0:7,0,0:70:0,70,371,70,371,371 0/1:9,10,0:99:117,0,289,356,319,675 0/0:6,0,0:85:0,85,310,85,310,310 0/1:4,7,0:99:250,0,129,262,150,412 0/0:20,0,0:72:0,72,1261,72,1261,1261 0/1:11,7,0:99:217,0,386,250,407,657 0/1:7,3,0:99:108,0,386,114,395,503 0/1:9,7,0:99:237,0,316,264,337,601 0/0:8,0,0:24:0,24,320,24,320,320 0/0:18,0,0:54:0,54,695,54,695,695 1/1:0,11,0:33:448,33,0,448,33,448 0/1:3,2,0:62:62,0,98,71,104,175 0/0:12,0,0:42:0,42,764,42,764,764 0/0:18,0,0:99:0,161,804,163,805,806 0/0:22,0,0:64:0,64,802,65,803,805 0/0:5,0,0:6:0,6,246,6,246,246 0/0:12,0,0:36:0,36,470,36,470,470 0/2:7,0,6:99:106,127,376,0,249,231 0/0:23,0,0:99:0,299,1169,299,1169,1169 0/0:13,0,0:39:0,39,512,39,512,512 0/0:18,0,0:54:0,54,693,54,693,693 0/1:3,4,0:97:137,0,97,146,109,255 0/0:13,0,0:39:0,39,506,39,506,506 0/0:7,0,0:21:0,21,276,21,276,276 0/0:19,0,0:99:0,127,958,127,958,958 0/0:7,0,0:21:0,21,240,21,240,240 0/0:27,0,0:83:0,83,1037,83,1037,1037 0/0:8,0,0:9:0,9,439,9,439,439>
no genotype for some sample:
SCF35 901454 . A G 7638.11 . AC=22;AF=0.333;AN=66;ActiveRegionSize=51;BaseQRankSum=12.776;ClippingRankSum=-3.046;DP=355;EVENTLENGTH=0;FS=34.579;HaplotypeScore=45.6947;InbreedingCoeff=-0.5098;MLEAC=22;MLEAF=0.333;MQ=88.52;MQ0=0;MQRankSum=-8.391;NVH=4;NumHapAssembly=9;NumHapEval=9;QD=31.05;QDE=7.76;ReadPosRankSum=-0.323;TYPE=SNP;extType=SNP GT:AD:GQ:PL 0/0:6,1:5:0,5,698 0/1:3,11:99:216,0,531 0/1:2,5:99:211,0,136 0/1:3,8:99:183,0,370 0/0:7,0:27:0,27,767 0/1:0,8:99:446,0,222 0/1:11,12:99:197,0,1491 0/1:9,3:99:172,0,1153 :15,0:75:0,75,1290 0/0:4,0:24:0,24,323 0/1:7,11:99:292,0,218 0/1:5,10:99:289,0,133 0/1:9,15:99:537,0,276 1/1:0,14:42:545,42,0 1/1:0,1:2:35,2,0 0/0:11,0:49:0,49,618 0/0:14,0:42:0,42,542 1/1:0,17:44:485,44,0 0/0:26,0:99:0,613,1675 0/1:3,3:91:91,0,94 0/1:10,8:99:189,0,555 0/1:3,14:99:395,0,141 0/1:7,3:99:120,0,387 ./. 0/0:15,0:99:0,147,675 0/1:1,3:29:104,0,29>
Best, SK