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Feature Request: Parallelize more GATK tools

bredesonbredeson Member ✭✭
edited June 2014 in Ask the GATK team

I have a feature request:

I'm a little surprised to find that the DepthOfCoverage tool still does not allow parallelization as of v3.1-1. Would it be possible to parallelize this tool and others that consider samples/BAMs data independent. Pretty please... :-)

Thanks!

ERROR ------------------------------------------------------------------------------------------
ERROR A USER ERROR has occurred (version 3.1-1-g07a4bf8):
ERROR
ERROR This means that one or more arguments or inputs in your command are incorrect.
ERROR The error message below tells you what is the problem.
ERROR
ERROR If the problem is an invalid argument, please check the online documentation guide
ERROR (or rerun your command with --help) to view allowable command-line arguments for this tool.
ERROR
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions http://www.broadinstitute.org/gatk
ERROR
ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.
ERROR
ERROR MESSAGE: Invalid command line: Argument nt has a bad value: The analysis DepthOfCoverage currently does not support parallel execution with nt. Please run your analysis without the nt option.
ERROR ------------------------------------------------------------------------------------------
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