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.

Mutect Build: Java requirements

noushin6noushin6 Baltimore, MDMember

Hello GATK team,

I am having a hard time trying to build mutect from the github repository, following the instructions at:

Here are my questions:

1) What are the requirements for the java environment; i.e. does Mutect compile using OpenJDK or Sun JDK?

2) More specifically, I am getting the following error when running "mvn -Ddisable.queue install":

[ERROR] Failed to execute goal
com.pyx4j:maven-junction-plugin:1.0.3:link (link-public-testdata) on
project sting-aggregator: Can't create junction source
-> [/mnt/hn05_disk001/test/gatk-protected/public/testdata] -> [Help 1]


Best Answers


Sign In or Register to comment.