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?