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.
GATK depth of coverage -L option
Hi GATK team
I am trying to use GATK depth of coverage program to obtain region wise coverage for my samples. I have whole exome seq data for normal and tumor, but done on different kits. When I run GATK depth of coverage program, which bed file would I use for the -L option? I require coverage for every region because I use this to obtain copy number using the ExomeCNV package in R. I would really appreciate any inputs.