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.
Bug reporting for MuTect
I believe there is a bug in MuTect's indel proximity filter. Specifically, in the way that it detects indels.
This was tested on precompiled 1.1.4 and 1.1.5. I have not tested the latest source code, but it looks like it's still there.
What's the procedure for reporting bugs?