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 source code debugging
I followed the instructions from your guide on how to make GATK from source with IntelliJ IDEA.
My only problem is that GenomeAnalysisTK.jar is not generated, and I don't know which class should I give to the debugger as the main class?