According to MuTect2s docs, the default is to downsample by sample to 1,000x. I would like to lower this substantially to something like 3,000 or lower. When I use the -dcov argument in my command line I get:
ERROR ------------------------------------------------------------------------------------------
ERROR A USER ERROR has occurred (version 3.5-0-g36282e4):
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: Cannot use -dcov or --downsample_to_coverage for ActiveRegionWalkers, use another downsampling argument
ERROR ------------------------------------------------------------------------------------------
Is there another way to adjust the downsampling in MuTect2?