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!
DepthOfCoverage memory usage
Is there a way to manage DepthOfCoverage memory usage? I am having problems when I give it a large intervals file. I can successfully run other tools like RealignerTargetCreator, IndelRealigner, and BaseRecalibrator, which seem like they would be more memory-intensive. I can also run DepthOfCoverage with
--omitIntervalStatistics --omitLocusTable --omitDepthOutputAtEachBase. However, running it with just
--omitDepthOutputAtEachBase gives me a memory error:
##### ERROR MESSAGE: There was a failure because you did not provide enough memory to run this program. See the -Xmx JVM argument to adjust the maximum heap size provided to Java
Is there any way to optimize that?