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Error in documentation

Wasn't able to comment on the specific page, but at:


there is an error in the documentation - specifically where it says in the example:

-T Coverage \

it should be:

-T DepthOfCoverage \

if you use Coverage, then GATK will complain with:

"ERROR MESSAGE: Invalid command line: Malformed walker argument: Could not find walker with name: Coverage"

Best Answers


  • Gavin_SherlockGavin_Sherlock StanfordMember

    Also, the documentation suggests that the -nt option can be used, but when I used it, I got:

    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.
  • Gavin_SherlockGavin_Sherlock StanfordMember

    Thanks - that worked.

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