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Genotype with depth but no coverage of either of alleles?

crop_bioinfocrop_bioinfo knoxvilleMember
edited February 2017 in Ask the GATK team

Hello I used Haplotypecaller, extracted SNP and did hard filtering. I can see genotype without allele coverage. I was wondering about the issue? Please check the last sample. Also, please check the last locus which has all 0,0,0 but still has genotype.

`5_LG10 5899 . C A 1132.94 PASS AC=3;AF=0.188;AN=16;BaseQRankSum=2.973;ClippingRankSum=0.000;DP=432;ExcessHet=3.9794;FS=0.000;MLEAC=3;MLEAF=0.188;MQ=60.00;MQRankSum=0.000;QD=7.87;ReadPosRankSum=-0.134;SOR=0.603 GT:AD:DP:GQ:PL 0/1:28,6:34:99:189,0,1128 0/1:41,11:52:99:327,0,1683 0/0:28,0:28:85:0,85,1241 0/0:125,0:125:99:0,386,5698 0/0:46,1:47:99:0,133,2055 0/1:39,19:58:99:660,0,1570 0/0:62,0:62:99:0,188,2760 0/0:.:.:15:0,15,122

5_LG10 51133 . C G 648.78 PASS AC=4;AF=0.250;AN=16;BaseQRankSum=1.978;ClippingRankSum=0.000;DP=453;ExcessHet=0.9691;FS=0.000;MLEAC=4;MLEAF=0.250;MQ=60.00;MQRankSum=0.000;QD=8.32;ReadPosRankSum=1.112;SOR=0.786 GT:AD:DP:GQ:PL 0/1:40,7:47:99:174,0,1659 0/1:23,8:31:99:303,0,946 0/0:28,0:28:87:0,87,1274 0/0:162,0:162:99:0,506,7411 0/0:42,0:42:99:0,132,1939 0/0:45,0:45:99:0,141,2111 0/0:96,0:96:99:0,307,4528 1/1:.:.:27:223,27,0

7_LG14 19112 . G A 13977.40 PASS AC=9;AF=0.563;AN=16;BaseQRankSum=2.485;ClippingRankSum=0.000;DP=1588;ExcessHet=13.4916;FS=2.082;MLEAC=9;MLEAF=0.563;MQ=60.00;MQRankSum=0.000;QD=8.80;ReadPosRankSum=-4.164;SOR=0.854 GT:AD:DP:GQ:PL 0/1:77,42:119:99:1571,0,3146 0/1:62,40:102:99:1607,0,2642 0/1:39,29:68:99:1088,0,1718 0/1:461,98:559:99:3039,0,19945 0/1:187,42:229:99:1398,0,8463 0/1:144,52:196:99:1864,0,6049 0/1:227,88:315:99:3363,0,9616 1/1:.:.:6:90,6,0

8_LG16 12482 . G T 5190.53 PASS AC=8;AF=0.500;AN=16;BaseQRankSum=5.913;ClippingRankSum=0.000;DP=465;ExcessHet=2.5225;FS=4.534;MLEAC=9;MLEAF=0.563;MQ=60.00;MQRankSum=0.000;QD=15.00;ReadPosRankSum=1.493;SOR=0.980 GT:AD:DP:GQ:PL 0/1:4,30:34:78:1248,0,78 0/1:7,12:19:99:473,0,227 1/1:0,12:12:36:537,36,0 0/1:151,35:186:99:1015,0,6146 0/1:47,10:57:99:278,0,1923 1/1:0,38:38:99:1690,114,0 0/0:119,0:119:99:0,361,5339 0/0:.:.:3:0,3,45

33_LG12 5958 . C T 1594.51 PASS AC=2;AF=0.125;AN=16;BaseQRankSum=-1.364;ClippingRankSum=0.000;DP=567;ExcessHet=0.1472;FS=0.893;MLEAC=2;MLEAF=0.125;MQ=60.00;MQRankSum=0.000;QD=27.49;ReadPosRankSum=0.689;SOR=0.740 GT:AD:DP:GQ:PL 0/0:61,0:61:99:0,181,2060 0/0:28,0:28:83:0,83,905 0/0:33,0:33:99:0,99,1135 0/0:186,1:187:99:0,516,5774 0/0:74,0:74:99:0,222,1990 1/1:1,57:58:99:1640,162,0 0/0:123,0:123:99:0,375,4082 0/0:.:.:36:0,36,297

35_LG16 5143 . G A 6176.02 PASS AC=3;AF=0.188;AN=16;BaseQRankSum=-2.397;ClippingRankSum=0.000;DP=443;ExcessHet=3.9794;FS=0.540;MLEAC=3;MLEAF=0.188;MQ=60.00;MQRankSum=0.000;QD=22.87;ReadPosRankSum=-0.227;SOR=0.642 GT:AD:DP:GQ:PL 0/0:49,0:49:99:0,150,2180 0/0:31,0:31:93:0,93,1362 0/0:21,0:21:63:0,63,945 0/1:48,104:152:99:4177,0,1724 0/1:28,22:50:99:806,0,1089 0/1:36,32:68:99:1235,0,1401 0/0:70,2:72:99:0,127,3049 0/0:.:.:3:0,3,25

38_LG10 10705 . T G 1193.86 PASS AC=3;AF=0.188;AN=16;BaseQRankSum=5.479;ClippingRankSum=0.000;DP=553;ExcessHet=3.9794;FS=2.669;MLEAC=3;MLEAF=0.188;MQ=60.00;MQRankSum=0.000;QD=11.48;ReadPosRankSum=-2.171;SOR=1.163 GT:AD:DP:GQ:PL 0/1:31,19:50:99:685,0,1367 0/1:24,13:37:99:474,0,969 0/1:15,2:17:78:78,0,621 0/0:207,0:207:99:0,650,9686 0/0:76,0:76:99:0,235,3469 0/0:71,0:71:99:0,217,3209 0/0:95,0:95:99:0,289,4306 0/0:.:.:33:0,33,495

62_LG04 5032 . G A 1908.51 PASS AC=2;AF=0.125;AN=16;BaseQRankSum=0.674;ClippingRankSum=0.000;DP=452;ExcessHet=0.1472;FS=0.000;MLEAC=2;MLEAF=0.125;MQ=60.00;MQRankSum=0.000;QD=30.17;ReadPosRankSum=0.384;SOR=0.694 GT:AD:DP:GQ:PL 0/0:37,0:37:99:0,111,1665 0/0:40,0:40:99:0,123,1832 0/0:15,0:15:57:0,57,784 0/0:142,0:142:99:0,436,6480 0/0:54,0:54:99:0,169,2478 1/1:0,43:43:99:1954,132,0 0/0:121,0:121:99:0,379,5590 0/0:.:.:39:0,39,585

62_LG04 5831 . G C 1168.27 PASS AC=1;AF=0.063;AN=16;BaseQRankSum=4.230;ClippingRankSum=0.000;DP=455;ExcessHet=3.0103;FS=1.107;MLEAC=1;MLEAF=0.063;MQ=60.00;MQRankSum=0.000;QD=12.84;ReadPosRankSum=-3.774;SOR=0.779 GT:AD:DP:GQ:PL 0/0:49,0:49:99:0,151,2250 0/0:43,0:43:99:0,129,1818 0/0:21,0:21:63:0,63,934 0/0:111,0:111:99:0,334,4975 0/0:45,0:45:99:0,138,2029 0/1:60,31:91:99:1202,0,2462 0/0:95,0:95:99:0,298,4455 0/0:.:.:45:0,45,675

64_LG10 1122 . C T 200.58 PASS AC=2;AF=0.125;AN=16;BaseQRankSum=-0.632;ClippingRankSum=0.000;DP=474;ExcessHet=3.3099;FS=5.851;MLEAC=2;MLEAF=0.125;MQ=60.00;MQRankSum=0.000;QD=2.91;ReadPosRankSum=0.610;SOR=1.439 GT:AD:DP:GQ:PL 0/1:24,8:32:99:119,0,791 0/1:30,7:37:99:120,0,1060 0/0:29,3:32:2:0,2,972 0/0:151,0:151:99:0,452,5019 0/0:48,0:48:99:0,144,1384 0/0:89,0:89:99:0,270,3157 0/0:85,0:85:99:0,254,2455 0/0:.:.:24:0,24,360

120_LG16 12996 . G A 883.42 PASS AC=1;AF=0.063;AN=16;BaseQRankSum=-0.191;ClippingRankSum=0.000;DP=556;ExcessHet=3.0103;FS=2.512;MLEAC=1;MLEAF=0.063;MQ=60.00;MQRankSum=0.000;QD=13.19;ReadPosRankSum=0.076;SOR=0.935 GT:AD:DP:GQ:PL 0/0:59,0:59:99:0,176,1999 0/0:44,0:44:99:0,132,1518 0/0:29,0:29:86:0,86,948 0/0:156,0:156:99:0,468,4656 0/0:74,0:74:99:0,222,1920 0/1:30,37:67:99:917,0,652 0/0:105,0:105:99:0,315,2906 0/0:0,0:0:9:0,9,74
`

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