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.
to report a little typo
I am new to the GATK forum and I am not sure It's the right place I am posting to so all my apologies if I am in the wrong place. However, I wanted just to report a little typo that occurs here:
Actually, within the usage example box, the "known" argument is written as follow:
Well, if you execute it as it is, it produces the ERROR MESSAGE: Argument with name 'known' isn't defined.
In fact, and according to the same link, for IndelRealigner you should use either --knownAlleles or -known instead of the --known argument which work well for RealignerTargetCreator.
All the best.