Heads up:
We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
Notice:
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!
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.
Attention:
We will be out of the office for a Broad Institute event from Dec 10th to Dec 11th 2019. We will be back to monitor the GATK forum on Dec 12th 2019. In the meantime we encourage you to help out other community members with their queries.
Thank you for your patience!
We will be out of the office for a Broad Institute event from Dec 10th to Dec 11th 2019. We will be back to monitor the GATK forum on Dec 12th 2019. In the meantime we encourage you to help out other community members with their queries.
Thank you for your patience!
GATK source code debugging

Hi,
I followed the instructions from your guide on how to make GATK from source with IntelliJ IDEA.
My only problem is that GenomeAnalysisTK.jar is not generated, and I don't know which class should I give to the debugger as the main class?
Answers
@pcdeni
Hi,
You can download the GATK here: https://www.broadinstitute.org/gatk/download/
-Sheila
Dear Sheila,
I downloaded the source code from github.
Then I followed your instructions from guide » developer zone » Setting up your dev environment: Maven and IntelliJ for GATK 3+
And now I have the source code in the IDE, and I can even make it, but if I try to modify something, then I have to set the main class (for ex. for debugging), and I don't know which is the main class, because GenomeAnalysisTK.jar is not among the source files, and there is no corresponding .java or .class file.
Thanks.
@pcdeni
Hi,
I hope this will answer your question. I had to ask some of our software engineers @thibault @ronlevine
First you have to build the executable from the source code mvn verify -P!queue
The executable is: target/GenomeAnalysisTK.jar
Then setup IntelliJ: http://gatkforums.broadinstitute.org/discussion/4023/setting-up-your-dev-environment-maven-and-intellij-for-gatk-3
If you are debugging remotely: http://gatkforums.broadinstitute.org/discussion/4712/howto-set-up-remote-debugging-in-intellij
-Sheila