If you happen to see a question you know the answer to, please do chime in and help your fellow community members. 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.
Custom Walker Distribution and command line
I'm planning to write custom walkers for the GATK public framework (using a Maven dependency with jitpack.io) and distribute that software including the custom walkers as a jar file with dependencies, where the only available walkers from the command line will be the custom ones. Although in the logging for my command line will be the version of the GATK framework in use, I would like to use a different logging for the beginning of the program and the error (instead of the link to the GATK webpage), so I will need to create and/or extend classes from the GATK engine (for the command line).
Of course, the software will be open source (MIT license), but I wonder if it could be possible to distribute a software in such a way. In addition, I would like to know if it is possible for the developers to made a tutorial on how to start the GATK engine with a custom walker without using the GATK command line.
Thank you very much in advance.