DepthOfCoverage multi-threading
Posted in Ask the GATK team | Last updated on


Comments (2)

Does the walker DepthOfCoverage support multi-threading?

According to the documentation: http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_coverage_DepthOfCoverage.html "This tool can be run in multi-threaded mode using this option. TreeReducible (-nt)"

When I try with GATK2.5 I get this error message: "Invalid command line: Argument nt has a bad value: The analysis DepthOfCoverage aggregates results by interval. Due to a current limitation of the GATK, analyses of this type do not currently support parallel execution. Please run your analysis without the -nt option."

Would it work, if I upgraded to 2.7? You upgrade GATK more frequently than I change my under wear, so it is difficult to keep up :) Thanks!


Return to top Comment on this article in the forum