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.
We will be out of the office on November 11th and 13th 2019, due to the U.S. holiday(Veteran's day) and due to a team event(Nov 13th). We will return to monitoring the GATK forum on November 12th and 14th respectively. Thank you for your patience.

FYI: GATK is able to complete all my workflows using OpenJDK 11.0.4

SkyWarriorSkyWarrior TurkeyMember ✭✭✭


I wanted to inform the devs and the community that the latest version of GATK is able to complete all my local workflows using OpenJDK 11.0.4 (AdoptOpenJDK). This was tested on Debian 10 and I was wondering if this is due to the updated HTSJDK which states in the github that 2.20 is tested against Java 11 as well. Unfortunately I was unable to compile the GATK package using Java 11 (albeit htsjdk compiles successfully under Java 11 !) but running under Java 11 does not seem to cause any issues.

Just my 2 cents on this matter.



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