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.
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 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!

SplitNCigarReads uses more than 1 core with no options to set number of cores used

If running on a cluster system that kills jobs if they use more than their allocation, you need to be able to either know how many cores are required or be able to limit the number of cores used. Are there options I am missing? Otherwise I would like to know the recommended number of cores to request for this tool. Is the number of cores used based on what the machine has? If so that needs to be limited for a cluster or cloud system. Right now I am requesting 4 cores per job but the jobs spend most of their time at < 200% CPU usage.


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