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.
Spark in other clusters?
After experiencing some issues with GATK 3.2 on CentOS 7.4 (AVX changes broke everything), we've installed the newer versions - 3.8.
I thought I'd install 4 beta to test, but am confused by all this talk of SPARK.
We run a SLURM cluster. Do I need to install SPARK to run on top of that in order to get the advantages, or is SPARK not strictly necessary for running on a cluster?
That being the case - can we delete the gatk-package-4.beta.5-spark.jar?
(to my shame I found the answer in this tutorial after asking the question)