Does the walker DepthOfCoverage support multi-threading?
According to the documentation:
"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!