What argument(s) should be used instead of --debug-graph-transformations?

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ISmolicz

• June 08, 2023 21:46
• Edited

Hello GATK Team,

The documentation entitled 'When HaplotypeCaller and Mutect2 do not call an expected variant' suggests running Mutect2 with the argument --debug-graph-transformations set as true as a later option in troubleshooting for the issue discussed in this documentation. However, this argument is not available in later versions of Mutect2, including the current version.

Which argument(s) should be used instead (e.g. --assembly-region-out, --debug-assembly, --graph-output, --pair-hmm-results-file)? Should .dot files still be generated?

Thank you for your time and help.

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  David Benjamin

  • June 12, 2023 15:07

  I don't think we removd that argument, and I just ran the latest version of Mutect2 with the --debug-graph-transformations argument to double check.  What version of GATK were you using, and what was your command?

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  ISmolicz

  • June 13, 2023 10:04

  Thank you for your reply David Benjamin.

  Apologies, I did not realise it was still an existing argument as it was not listed in the Mutect2 documentation argument list. My colleague ran the command without an error, but there were no different outputs or logs. I will check again.

  Please can I just confirm that only .dot files should be the extra files generated?

  Thank you again.

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  David Benjamin

  • June 14, 2023 01:42

  Yes, just a lot of .dot files.

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