Is FilterAlignmentArtifacts out of the Mutect2 calling best practices?

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shenglai

• March 11, 2022 01:53

Hi GATK team,

 

I notice that `FilterAlignmentArtifacts` is no longer part of the best practices when calling Mutect2. https://gatk.broadinstitute.org/hc/en-us/articles/360035531132--How-to-Call-somatic-mutations-using-GATK4-Mutect2

However, it looks like in the wdl, it's still calling it when providing the reference image. https://github.com/broadinstitute/gatk/blob/b14f810b91faf14d39e7e2810838e7bc55b73998/scripts/mutect2_wdl/mutect2.wdl#L332

I am curious why we remove `FilterAlignmentArtifacts` from the best practices, and if I was following the right wdl.

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  Genevieve Brandt (she/her)

  • March 30, 2022 17:35

  Hi shenglai,

  Yes, it looks like that WDL is the up to date Mutect2 WDL. You can always check on our Dockstore page, which is where we have all the up to date featured workspaces.

  The FilterAlignmentArtifacts is optional and only gets called when the user provides a realignment_index_bundle value.
  https://github.com/broadinstitute/gatk/blob/4.1.8.1/scripts/mutect2_wdl/mutect2.wdl#L38
  https://github.com/broadinstitute/gatk/blob/4.1.8.1/scripts/mutect2_wdl/mutect2.wdl#L360.

  Let me know if you have any further questions.

  Best,

  Genevieve

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