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.
Building MuTect 1.1.7?
I tried to build the latest MuTect according to the readme available at https://github.com/broadinstitute/mutect and I ran into an error. Specifically, there is an error building gatk-protected only if I include the git reset --hard 3.1.
git reset --hard 3.1
(comment) build the GATK first and install it to the local mvn repo.
mvn -Ddisable.queue install
If I do not include the git reset --hard 3.1 then gatk-protected will build fine, but then
(comment) build MuTect
does not work and reports errors about needing gatk repository/dependencies.
Has something changed recently that interferes with building MuTect, or am I doing something wrong?