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!
exome interval file for BaseCoverageDistribution
I would like to obtain the coverage distribution on all exome intervals (human reference genome) using the BaseCoverageDistribution function in GATK. The problem I'm having is finding an appropriate reference file to associate with the -L argument. Specifically, the standard UCSC exome coordinate file doesn't have a format that GATK will accept, e.g. (header and first row given below, as opposed to chr1:start-stop) etc
name chrom strand cdsStart cdsEnd exonCount exonStarts exonEnds name2 exonFrames
NM_017582 chr1 - 154522913 154531029 13 154521050,154523413,154523872,154524246,154524396,1545
54528440,154531120, UBE2Q1 1,0,0,2,0,2,1,0,0,0,0,0,0,