Mitochondrial analysis - FilterMutectCalls autosomal-coverage is not an option

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leory

• February 16, 2021 13:42

Hello GATK team,

Version: gatk-4.1.9.0
Command: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx6G -jar gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar FilterMutectCalls -V samp1_merged.vcf -R phaafr_MT.fa -O samp1_merged_filtered.vcf --stats raw.combined.stats --max-alt-allele-count 4 --mitochondria-mode --autosomal-coverage 9 --contamination-estimate 0.000
Error log:
***********************************************************************
A USER ERROR has occurred: autosomal-coverage is not a recognized option
***********************************************************************

I try to Filter mitochondrial variants with FilterMutectCalls. In the past there was an option called --autosomal-coverage (gatk-4.1.6.0 still has this), but it is not available any more in version gatk-4.1.9.0.
Can you please tell me why was this option removed and if there is any new options superseding this?

The most recent documentation:

https://gatk.broadinstitute.org/hc/en-us/articles/360051305471-FilterMutectCalls

still explicitly mentions this option:

"When running on unfiltered output of Mutect2 in --mitochondria mode, setting the advanced option --autosomal-coverage argument (default 0) activates a recommended filter against likely erroneously mapped NuMTs (nuclear mitochondrial DNA segments). For the value, provide the median coverage expected in autosomal regions with coverage."

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  Genevieve Brandt (she/her)

  • February 16, 2021 18:20

  Hi leory,

  It looks like there were some major changes to the mitochondria pipeline filtering in 4.1.7.0, you can find the release notes here: https://github.com/broadinstitute/gatk/releases/tag/4.1.7.0.

  There are notes at the pull request on github here: https://github.com/broadinstitute/gatk/pull/6399

  I will make a note with our documentation team to remove the mention of that option in the recent documentation, thank you for pointing that out!

  Best,

  Genevieve

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  leory

  • March 16, 2021 09:56

  Hi Genevieve,

  I have compared the called MT variants with the --autosomal-coverage option with FilterMutectCalls (v.4.1.6) and FilterMutectCalls, MTLowHeteroplasmyFilterTool and NuMTFilterTool. The results are broadly consistent, the only big difference I observed was in the case of a single sample with low coverage (autosomal <10x) where the previous FilterMutectCalls with --autosomal-coverage filtered out more than 75% of the raw variants (as opposed to ~50% of the high coverage samples). 
  The new tools looks great, can you please ask the documentation team to add entries for MTLowHeteroplasmyFilterTool and NuMTFilterTool as well?

  Thank you for the links describing the changes in the MT variant filtration steps.

  Best wishes,

  Lel

   

   

   

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  Genevieve Brandt (she/her)

  • March 20, 2021 03:49

  Hi Lel,

  Thank you for the feedback, and I am so glad it is working for you! I will work with our user education team to build better documentation for those tools.

  Genevieve

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