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.
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?