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Test-drive the GATK tools and Best Practices pipelines on Terra
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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?