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.
Fallback and documentation for GATK tools that don't support multithreading
I've been using the GATK - in particular, the DiagnoseTargets and VariantsToTable tools - and have been running into trouble attempting to parallelise these tasks.
I've tried both the -n and -nct flags and it turns out that neither are supported by the above tools. Unfortunately there doesn't appear to be anything on the documentation that indicates this, so I only ever find out the hard way when trying to run them. As such, I have a couple of questions:
Does the documentation list which of the engine-wide parameters are unsupported by certain tools? If not, could it?
Even if the tools aren't automagically parallelisable, I still want to run them -- it's a little frustrating to kick off a long-running process over the weekend and get back on Monday to find it failed a few hours in! Is there an option to fall back to single-threaded execution if one of the multithreading flags isn't supported? If not, could there be?