We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!
Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
Too high QUAL scores in Haplotypecaller gvcf
I'm getting some too-high QUAL scores in my VCF, the whole file is full of weird scores in the tens of thousands:
CHROM POS ID REF ALT QUAL FILTER INFO FORMAT
chrM 73 . G A 27120.46 . BaseQRankSum=-8.22
120;QD=32.10;ReadPosRankSum=-3.840e-01 GT:AD:DP:GQ:PL 1/1:1,332:333:99:10644
,962,0 1/1:1,315:316:99:10159,913,0 0/0:118,0:118:99:0,120,1800 1/1:0,19
chrM 146 rs72619361 T C 16226.15 . DB;DP=1315
;MLEAC=2;MLEAF=0.200;MQ=57.18;MQ0=0;QD=34.24 GT:AD:DP:GQ:PL 0/0:338,0:338:99:0,1
20,1800 0/0:324,0:324:99:0,120,1800 0/0:118,0:118:99:0,120,1800 0/0:17
chrM 150 . T C 52405.15 . BaseQRankSum=0.310;ClippingRankSum=0.695;DP=1523;MLEAC=8;MLEAF=0.800;MQ=60.00;MQ0=0;MQRankSum=-4.940e-01;QD=30.63;ReadPosRankSum=-1.364e+00 GT:AD:DP:GQ:PL 1/1:0,421:421:99:14544,1264,0 1/1:0,415:415:99:14206,1244,0 0/0:118,0:118:99:0,120,1800 1/1:1,206:207:99:7027,586,0 1/1:0,356:356:99:16670,1132,0
chrM 152 rs117135796 T C 16299.15 . DB;DP=1495;MLEAC=2;MLEAF=0.200;MQ=57.18;MQ0=0;QD=29.09 GT:AD:DP:GQ:PL 0/0:409,0:409:99:0,120,1800 0/0:411,0:411:99:0,120,1800 0/0:118,0:118:99:0,120,1800 0/0:204,0:204:99:0,120,1800 1/1:0,352:352:99:16341,1102,0
chrM 194 . C T 12039.15 . BaseQRankSum=-1.325e+00;ClippingRankSum=-4.920e-01;DP=1754;MLEAC=2;MLEAF=0.200;MQ=60.00;MQ0=0;MQRankSum=-1.597e+00;QD=32.89;ReadPosRankSum=1.11 GT:AD:DP:GQ:PL 0/0:409,0:409:99:0,120,1800 0/0:411,0:411:99:0,120,1800 1/1:6,360:366:99:12081,883,0 0/0:204,0:204:99:0,120,1800 0/0:361,0:361:99:0,120,1800
It's just a 4x WGS file, nothing fancy.
Any idea of why this might be?