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.
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!

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.

memory requirements for GATK tools

Hi GATK team,

I have been running the BaseRecalibrator tool on a .bam file that is ~100 gb. My job was killed because the memory for the job exceeded the max memory I allotted (8 gb). I have doubled the memory to 16gb and I hope that resolves the issue.
I was wondering if there are guidelines for memory requirements for the various GATK tools (RealignmentTargetCreator, IndelRealigner, BaseRecalibrator, PrintReads, MuTect) specific for files of different sizes? (I searched the documentation but had trouble finding this information). For example, is it known if the BaseRecalibrator tool requires X amount of memory for a file that is 100 gb? This would help me a lot by saving me time in trouble-shooting the memory settings.

Thanks very much,
Steve

Best Answer

Answers

Sign In or Register to comment.