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.
We will be out of the office for a Broad Institute event from Dec 10th to Dec 11th 2019. We will be back to monitor the GATK forum on Dec 12th 2019. In the meantime we encourage you to help out other community members with their queries.
Thank you for your patience!
Error in running variant recalibration
I am using GATK variant re calibration , it works fine on SNPs but throws an error on indel file. The error and my sample file are as follows:
ERROR MESSAGE: Your input file has a malformed header: The FORMAT field was provided but there is no genotype/sample data
##contig=<ID=17.5307,length=909> ##contig=<ID=17.5308,length=865> #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Q11 Q11D1 Q11D2 Q11D4 Q11D5 1.1 1773 . TTTTGAAATATTTAGATAA T 407.08 . AC=1;AF=0.167;AN=6;BaseQRankSum=-1.076e+00;ClippingRankSum=0.00;DP=104;ExcessHet=3.0103;FS=12.041;MLEAC=1;MLEAF=0.167;MQ=56.82;MQRankSum=1.75;QD=25.44;ReadPosRankSum=1.21;SOR=1.402 GT:AD:DP:GQ:PL 0/0:55,0:55:99:0,108,1620 0:11,0:11:99:0,253 0:13,0:13:99:0,357 0:9,0:9:99:0,204 1:3,13:16:99:450,0 1.1 1792 . CTTTAAAAGAAAATACTGGACAATTTTTTGATTTGAATTGGTTTTGAAATATGAATATATTGTATAATATGAGATTAAGGTAAATTATTGAAATTCAATATATATGACATTCTTATTCTTTTTTCTGGGTTTTTTGATGATT C 407.08 . AC=1;AF=0.167;AN=6;BaseQRankSum=-6.730e-01;ClippingRankSum=1.35;DP=99;ExcessHet=3.0103;FS=12.041;MLEAC=1;MLEAF=0.167;MQ=56.82;MQRankSum=1.35;QD=25.44;ReadPosRankSum=2.56;SOR=1.402 GT:AD:DP:GQ:PL 0/0:50,0:50:55:0,55,1227 0:11,0:11:99:0,253 0:13,0:13:99:0,357 0:9,0:9:99:0,204 1:3,13:16:99:450,0