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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.
Mutect2 out of memory - not enough java heap space
I am running Mutect2 on whole genome sequencing and have run into an error with java. It seems to be running out of heap space towards the end of the run. I plan to add more with the -Xmx option and also spread the jobs out with intervals. However, I am wondering if there is a way to predict or determine how much heap space is actually needed for a Mutect2 run.