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AD field has too many values for Biallelic site:

aeonsimaeonsim Member ✭✭✭
edited June 2014 in Ask the GATK team

Hi

I've just noticed this in some records, in some bi-allelic sites the AD field for some samples can have far more than 2 columns and the values can be separated oddly. For example in the record at the bottom of the 0/1:21,11,0,0,0:32:99:398,0,677 the site is biallelic so I'd expect the AD to be 21,11 with a DP of 32, but instead we have 21,11,0,0,0.

Then at another position here we have 0/1:12,0,9,0,0:21:99:220,0,792 with the AD 12,0,9,0,0 DP 21 when I would have expected to see AD 12,9 DP 21. The 0 between the ref and alt alleles is particularly troubling.

 chr1    110326664       rs209200395     A       C       20726.45        .       AC=65;AF=0.192;AN=338;BaseQRankSum=1.05;ClippingRankSum=-6.610e-01;DB;DP=3547;FS=0.000;InbreedingCoeff=0.0055;MLEAC=66;MLEAF=0.195;MQ=60.00;MQ0=0;MQRankSum=-3.900e-02;QD=16.71;ReadPosRankSum=0.638    GT:AD:DP:GQ:PL  0/0:.:5:15:0,15,156     0/0:.:2:6:0,6,69        0/0:.:23:60:0,60,900    0/0:.:9:27:0,27,275     0/0:.:26:63:0,63,945    0/0:.:41:99:0,102,1433  0/0:.:23:60:0,60,774    0/0:.:23:60:0,60,900    0/0:.:6:9:0,9,135       0/0:.:3:9:0,9,86        0/0:.:6:12:0,12,180     0/0:.:9:24:0,24,288     0/0:.:3:6:0,6,90        0/1:21,11,0,0,0:32:99:398,0,677 0/0:.:29:61:0,61,939    0/1:9,11,0,0,0:20:99:350,0,241  0/0:.:26:43:0,43,832    0/0:.:22:63:0,63,945    0/0:.:30:68:0,68,916    0/0:.:21:57:0,57,855    0/0:.:23:62:0,62,719    0/1:10,14,0,0,0:24:99:509,0,270 1/1:0,23,0,0,0:23:85:1001,85,0  0/1:18,13,0,0,0:31:99:426,0,485 0/0:.:25:68:0,68,812    0/1:17,10,0,0,0:27:99:357,0,518 0/0:.:38:72:0,72,1223   0/0:.:25:64:0,64,823    0/0:.:22:60:0,60,900    0/0:.:21:60:0,60,707    0/1:3,6,0,0,0:9:86:184,0,86     0/0:.:25:60:0,60,900    0/0:.:26:72:0,72,1080   0/0:.:22:60:0,60,900    0/0:.:37:81:0,81,1257   0/0:.:24:65:0,65,838    0/0:.:32:65:0,65,1055   0/0:.:32:73:0,73,1069   0/1:8,0,12,0,0:20:99:467,0,494  0/0:.:22:60:0,60,900    0/1:3,3,0,0,0:6:81:197,0,81     0/1:8,12,0,0,0:20:99:369,0,228  0/0:.:19:26:0,26,615    0/0:.:21:60:0,60,761    1/1:0,24,0,0,0:24:60:984,60,0   0/0:.:24:60:0,60,900    0/0:.:21:60:0,60,747    0/0:.:34:87:0,87,1166   0/0:.:21:60:0,60,701    0/0:.:19:41:0,41,646    0/0:.:21:63:0,63,720    0/0:.:18:29:0,29,609    0/0:.:26:69:0,69,1035   0/1:8,3,0,0,0:11:99:104,0,229   0/0:.:23:60:0,60,900    0/0:.:20:60:0,60,681    0/1:7,0,8,0,0:15:99:327,0,517   0/0:.:2:6:0,6,68        ./.:.:0 0/0:.:31:66:0,66,1067   0/0:.:2:6:0,6,44        0/0:.:3:9:0,9,87        0/0:.:2:6:0,6,66        0/0:.:1:3:0,3,30        0/0:.:2:6:0,6,68        0/0:.:18:26:0,26,583    0/0:.:2:6:0,6,64        0/1:3,5,0,0,0:8:79:150,0,79     0/0:.:2:6:0,6,65        0/0:.:5:15:0,15,150     0/1:11,13,0,0,0:24:99:445,0,323 0/0:.:49:75:0,75,1662   0/1:7,11,0,0,0:18:99:328,0,172  0/0:.:22:63:0,63,753    0/1:11,11,0,0,0:22:99:400,0,313 0/0:.:35:37:0,37,1051   0/0:.:24:66:0,66,990    0/1:10,0,16,0,0:26:99:542,0,538 0/0:.:23:63:0,63,945    0/0:.:21:60:0,60,900    0/1:7,0,5,0,0:12:99:149,0,507   0/0:.:29:74:0,74,990    0/0:.:2:0:0,0,4 0/1:5,12,0,0,0:17:99:397,0,148  0/1:8,0,11,0,0:19:99:364,0,489  0/0:.:11:27:0,27,405    0/1:10,16,0,0,0:26:99:508,0,259 0/1:9,0,6,0,0:15:99:253,0,579   0/0:.:28:54:0,54,894    0/1:16,6,0,0,0:22:99:198,0,460  0/0:.:26:60:0,60,886    0/1:9,8,0,0,0:17:99:270,0,238   0/0:.:30:78:0,78,1170   0/1:9,14,0,0,0:23:99:442,0,246  0/0:.:17:21:0,21,531    0/0:.:25:64:0,64,832    0/0:.:30:65:0,65,1002   0/0:.:28:65:0,65,926    ./.:.:0 0/0:.:2:6:0,6,64        0/1:8,9,0,0,0:17:99:320,0,216   0/0:.:2:6:0,6,56        0/1:12,14,1,0,0:27:99:419,0,351 0/0:.:29:81:0,81,1215   0/1:12,0,12,0,0:24:99:307,0,782 0/0:.:24:69:0,69,809    0/0:.:23:60:0,60,900    0/0:.:28:62:0,62,990    0/1:9,0,8,0,0:17:99:357,0,776   1/1:0,10,0,0,0:10:32:355,32,0   1/1:0,12,0,0,0:12:35:435,35,0   0/1:15,13,0,0,0:28:99:418,0,442 0/1:10,0,9,0,0:19:99:326,0,845  0/0:.:29:61:0,61,970    0/0:.:27:60:0,60,900    0/0:.:33:61:0,61,1049   0/1:12,13,0,0,0:25:99:416,0,361 0/0:.:25:69:0,69,1035   0/1:10,13,0,0,0:23:99:451,0,269 0/1:21,14,0,0,0:35:99:441,0,599 0/0:.:12:22:0,22,376    0/1:10,14,0,0,0:24:99:457,0,273 0/1:10,0,14,0,0:24:99:525,0,646 0/1:15,12,0,0,0:27:99:319,0,416 0/1:5,8,0,0,0:13:99:297,0,123   0/0:.:14:7:0,7,411      0/0:.:18:19:0,19,515    0/0:.:21:63:0,63,745    0/0:.:27:72:0,72,1080   0/1:17,8,0,0,0:25:99:358,0,478  0/1:11,15,0,0,0:26:99:627,0,290 0/0:.:16:13:0,13,506    0/0:.:21:60:0,60,900    0/1:10,0,19,0,0:29:99:579,0,793 0/0:.:33:63:0,63,1077   0/0:.:13:39:0,39,432    0/0:.:8:18:0,18,270     1/1:0,15,0,0,0:15:54:630,54,0   0/0:.:9:27:0,27,297     0/0:.:31:62:0,62,1030   1/1:0,17,0,0,0:17:50:601,50,0   0/0:.:31:59:0,59,977    0/1:18,16,0,0,0:34:99:550,0,526 0/0:.:24:61:0,61,796    0/0:.:9:27:0,27,296     0/1:5,5,0,0,0:10:99:206,0,103   0/1:17,11,0,0,0:28:99:406,0,511 0/1:8,9,0,0,0:17:99:241,0,224   0/0:.:13:33:0,33,495    0/0:.:44:84:0,84,1358   0/0:.:13:20:0,20,495    0/0:.:15:21:0,21,387    0/1:17,6,0,0,0:23:99:117,0,498  0/1:18,13,0,0,0:31:99:451,0,519 1/1:0,34,0,0,0:34:99:1375,116,0 0/0:.:18:32:0,32,564    0/0:.:16:20:0,20,535    0/0:.:29:62:0,62,995    0/1:13,0,4,0,0:17:92:92,0,740   0/0:.:17:21:0,21,559    0/0:.:30:57:0,57,1006   0/0:.:23:60:0,60,900    0/1:12,0,9,0,0:21:99:220,0,792  0/0:.:30:56:0,56,967    0/0:.:23:63:0,63,945    0/0:.:29:69:0,69,999    0/1:8,12,0,0,0:20:99:412,0,237  0/0:.:26:60:0,60,980    0/0:.:27:62:0,62,872    0/1:19,9,0,0,0:28:99:285,0,587  0/1:15,14,0,0,0:29:99:422,0,430
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