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.
New doc for developers regarding sting -> gatk renaming in 3.2
If you're a developer who uses the GATK framework, you may have noticed that the 3.2 release broke existing third-party walkers. This happened because we had to do some codebase-wide refactoring/renaming that changes package names and classpaths (most obviously, renaming all instances of "sting" to "gatk"). We're sorry for the inconvenience but this was necessary as a preparation step on the road to providing GATK as a maven artifact.
We have posted a document that details the changes and explains how to update third-party code to work with GATK framework versions 3.2 onward here.
While we're on this topic, it seems that the IntelliJ set up instructions are a little outdated (in part due to the renaming), so we'll be updating that as well in the near future.