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Is the parallelism documentation for DepthOfCoverage correct?
states (bold is my emphasis):
This tool can be run in multi-threaded mode using this option.
Yet when I run the GATK with
-nt, I get an error that
-nt is not supported (truncated to save space):
ERROR A USER ERROR has occurred (version 2.8-1-g932cd3a):
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.