Hi I've just been having a go with the new Haplotype Caller method and I've getting some odd or malformed lines in the VCF file for example:
For example the format line has declared we should have 4 fields for each Sample record but instead we have samples with 2 records.
Two examples are shown here:
See Block 1
GT:DP:GQ:PL 1/1:.:3:32,3,0 ./.:0
Or where the format block declares 5 fields and we get 3 instead:
GT:AD:DP:GQ:PL 0/0:1,1,0,0,0,0,0,0,0:2:3:0,3,24,3,24,24 ./.:.:0 0/0:1,0,0,0,0,0,0,0,0:1:1:0,1,40,3,41,43 ./.:.:3
Full blocks, Block 1
chr1 3489714 . G A 9667.23 . AC=154;AF=1.00;AN=154;DP=0;FS=0.000;InbreedingCoeff=-0.0391;MLEAC=154;MLEAF=1.00;MQ=0.00;MQ0=0;EFF=INTRAGENIC(MODIFIER|||||TIAM1||CODING|||1),INTRON(MODIFIER||||649|TIAM1|protein_coding|CODING|ENSBTAT00000064124|1|1);CSQ=A|ENSBTAG00000017839|ENSBTAT00000064124|Transcript|intron_variant||||||||1/5||1|TIAM1|HGNC| GT:DP:GQ:PL 1/1:.:3:32,3,0 1/1:.:18:207,18,0 1/1:.:6:78,6,0 1/1:.:12:140,12,0 1/1:.:9:101,9,0 ./.:0 1/1:.:9:97,9,0 1/1:.:9:96,9,0 1/1:.:21:244,21,0 1/1:.:12:138,12,0 1/1:.:12:124,12,0 1/1:.:9:105,9,0 1/1:.:15:164,15,0 1/1:.:15:153,15,0 1/1:.:27:265,27,0 1/1:.:12:125,12,0 1/1:.:18:214,18,0 ./.:0 1/1:.:9:108,9,0 1/1:.:15:169,15,0 ./.:0 1/1:.:6:76,6,0 1/1:.:6:66,6,0 1/1:.:12:140,12,0 1/1:.:3:28,3,0 1/1:.:3:10,3,0 1/1:.:12:128,12,0 ./.:0 1/1:.:18:181,18,0 1/1:.:9:98,9,0 1/1:.:15:161,15,0 1/1:.:15:185,15,0 1/1:.:12:133,12,0 1/1:.:15:175,15,0 1/1:.:18:178,18,0 1/1:.:12:133,12,0 1/1:.:9:105,9,0 1/1:.:12:141,12,0 1/1:.:15:166,15,0 1/1:.:9:108,9,0 1/1:.:15:160,15,0 1/1:.:27:267,27,0 1/1:.:21:218,21,0 1/1:.:9:107,9,0 1/1:.:3:28,3,0 1/1:.:9:80,9,0 1/1:.:6:46,6,0 ./.:0 1/1:.:6:61,6,0 1/1:.:21:241,21,0 1/1:.:15:161,15,0 1/1:.:6:82,6,0 1/1:.:12:143,12,0 1/1:.:9:109,9,0 1/1:.:21:249,21,0 1/1:.:6:40,6,0 1/1:.:9:94,9,0 1/1:.:15:185,15,0 1/1:.:12:129,12,0 1/1:.:12:132,12,0 ./.:0 1/1:.:21:207,21,0 1/1:.:12:136,12,0 1/1:.:12:109,12,0 1/1:.:18:192,18,0 ./.:0 1/1:.:9:68,9,0 1/1:.:12:138,12,0 1/1:.:6:73,6,0 1/1:.:9:105,9,0 1/1:.:9:98,9,0 1/1:.:6:65,6,0 ./.:0 1/1:.:6:65,6,0 ./.:0 1/1:.:6:58,6,0 1/1:.:12:131,12,0 ./.:0 ./.:01/1:.:3:38,3,0 1/1:.:3:37,3,0 1/1:.:21:227,21,0 1/1:.:12:131,12,0 1/1:.:6:66,6,0 1/1:.:9:100,9,0 1/1:.:21:209,21,0 1/1:.:6:63,6,0 1/1:.:6:69,6,0
Block 2
chr1 55248 . ACCC A,CCCC 179.69 . AC=13,6;AF=0.100,0.046;AN=130;BaseQRankSum=0.736;ClippingRankSum=0.736;DP=347;FS=0.000;InbreedingCoeff=0.2231;MLEAC=10,4;MLEAF=0.077,0.031;MQ=53.55;MQ0=0;MQRankSum=0.736;QD=4.99;ReadPosRankSum=0.736;EFF=INTERGENIC(MODIFIER||||||||||1),INTERGENIC(MODIFIER||||||||||2);CSQ=-||||intergenic_variant||||||||||||| GT:AD:DP:GQ:PL 0/0:1,1,0,0,0,0,0,0,0:2:3:0,3,24,3,24,24 ./.:.:0 0/0:1,0,0,0,0,0,0,0,0:1:1:0,1,40,3,41,43 0/0:1,0,0,0,0,0,0,0,0:1:2:0,2,44,3,45,46 0/0:.:5:0:0,0,103,0,103,103 0/0:3,0,1,0,0,0,0,0,0:4:9:0,9,81,9,81,81 0/0:0,0,1,0,0,0,0,0,0:1:1:0,1,2,1,2,2 ./.:.:1 0/0:.:3:0:0,0,41,0,41,41 0/0:1,0,0,0,0,0,0,0,0:1:9:0,9,73,9,73,73 0/1:1,0,0,1,0,0,0,0,0:2:22:28,0,73,28,22,46 0/0:1,0,0,0,0,0,0,0,0:1:4:0,4,25,4,25,25 0/0:2,0,0,0,0,0,0,0,0:2:21:0,21,273,21,273,273 0/1:5,0,0,1,0,0,0,0,0:6:11:11,0,235,26,158,175 ./.:0,0,0,0,1,0,0,0,0:1 0/0:.:4:0:0,0,46,0,46,46 ./.:.:3 ./.:.:2 0/1:1,0,1,1,0,0,0,0,0:3:21:28,0,44,31,21,52 0/0:.:4:0:0,0,77,0,77,77 0/0:0,0,1,0,0,0,0,0,0:1:1:0,1,2,1,2,2 0/0:.:2:6:0,6,51,6,51,51 0/0:.:6:2:0,2,151,2,151,151 0/0:2,0,1,0,0,0,0,0,0:3:7:0,7,74,7,74,74 ./.:.:0 0/0:2,0,0,0,0,0,0,0,0:2:5:0,7,59,5,37,35 1/2:0,0,0,1,0,0,0,0,0:1:1:27,1,40,26,0,25 0/0:2,0,0,0,0,0,0,0,0:2:9:0,9,83,9,83,83 ./.:.:0 2/2:0,0,0,0,0,3,0,0,0:3:9:59,59,59,9,9,0 ./.:.:16 0/0:2,0,0,0,0,0,0,0,0:2:7:0,7,59,7,59,59 0/0:2,0,0,0,0,0,0,0,0:2:9:0,9,83,9,83,83 0/0:2,0,0,0,0,0,0,0,0:2:11:0,11,68,11,68,68 0/2:6,0,0,0,0,2,0,0,0:8:18:18,39,384,0,346,340 ./.:.:1 0/1:3,0,0,1,0,0,0,0,0:4:25:25,0,96,34,100,134 0/0:2,0,0,0,0,0,0,0,0:2:12:0,12,105,12,105,105 0/1:1,0,0,1,0,0,0,0,0:2:17:17,0,94,21,26,44 0/0:.:2:6:0,6,64,6,64,64 0/0:1,0,0,0,0,0,0,0,0:1:2:0,2,24,3,25,27 0/0:.:2:6:0,6,48,6,48,48 0/0:.:2:6:0,6,63,6,63,63 0/0:0,0,1,0,0,0,0,0,0:1:0:0,0,1,0,1,1 ./.:.:0 0/0:1,0,0,0,0,0,0,0,0:1:1:0,1,6,3,8,9 0/0:1,0,0,0,0,0,0,0,0:1:15:0,15,124,15,124,124 ./.:.:0 0/0:1,0,0,0,0,0,0,0,0:1:4:0,4,19,4,19,19 0/1:2,0,0,1,0,0,0,0,0:3:28:28,0,66,34,70,104 0/0:.:4:0:0,0,18,0,18,18 0/2:2,0,0,0,0,4,0,0,0:6:57:68,74,143,0,69,57 ./.:.:0 0/0:4,0,0,0,0,0,0,0,1:5:15:0,15,109,15,109,109 0/0:.:10:0:0,0,182,0,182,182 0/0:.:1:3:0,3,31,3,31,31 0/0:0,0,1,0,0,0,0,0,0:1:1:0,1,2,1,2,2 0/0:2,0,0,0,0,0,0,0,0:2:5:0,5,76,6,78,79 0/0:1,1,0,0,0,0,0,0,0:2:4:0,4,28,4,28,28 ./.:.:1 1/1:0,0,0,2,0,0,0,0,0:2:6:67,6,0,67,6,67 ./.:.:1 0/0:.:2:0:0,0,14,0,14,14 ./.:.:0 ./.:.:1 0/0:.:5:1:0,1,120,1,120,120 0/0:.:4:0:0,0,8,0,8,8 0/0:.:6:0:0,0,94,0,94,94 0/1:1,0,0,2,0,0,0,0,0:3:1:27,0,1,29,6,35 0/0:.:2:0:0,0,3,0,3,3 ./.:.:6 ./.:.:0 ./.:.:0 0/2:3,0,0,0,0,2,0,0,0:5:27:46,27,89,0,62,81 ./.:.:0 0/0:.:1:0:0,0,6,0,6,6 0/0:.:9:0:0,0,86,0,86,86 ./.:.:1 ./.:.:0 1/1:.:.:0:1,1,0,1,0,0 0/0:0,0,0,0,0,0,0,0,0:0:3:0,3,26,3,26,26 0/1:4,0,0,2,0,0,0,0,0:6:49:49,0,93,61,100,160 0/0:.:3:0:0,0,14,0,14,14 0/0:.:8:0:0,0,60,0,60,60 0/0:2,1,0,0,0,0,0,0,0:3:6:0,6,37,6,37,37 ./.:.:2 0/0:.:9:0:0,0,81,0,81,81 0/0:0,0,0,0,0,0,0,0,0:0:1:0,1,2,1,2,2
Any idea what the issue is?
