If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.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.

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:

--known indels.vcf

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.



Issue · Github
by Sheila

Issue Number
Last Updated


Sign In or Register to comment.