using MUTECT2 on tumor-only sample

BogdanBogdan Palo Alto, CAMember

Dear all,

although this question has been asked a long time ago, if you do not mind asking it again, as I am looking for some updated workflows, strategies, ideas :

"what would be the acceptable pipeline for processing WES or WGS data from primary tumors that do not have matched germlines sequences ?"

thanks a lot,

-- bogdan

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Best Answers

  • shleeshlee Cambridge admin
    Accepted Answer

    Hi @Bogdan,

    For somatic SNV and indel calling, GATK4-Mutect2 (and FilterMutectCalls) is what we offer. See here for M2 documentation.

    As you know, SNVs and indels are only part of the tumor story. You should check out our somatic CNV calling pipeline to fill in the other half of the picture, e.g. with Tutorial#9143.

Answers

  • shleeshlee CambridgeMember, Administrator, Broadie, Moderator admin
    Accepted Answer

    Hi @Bogdan,

    For somatic SNV and indel calling, GATK4-Mutect2 (and FilterMutectCalls) is what we offer. See here for M2 documentation.

    As you know, SNVs and indels are only part of the tumor story. You should check out our somatic CNV calling pipeline to fill in the other half of the picture, e.g. with Tutorial#9143.

  • BogdanBogdan Palo Alto, CAMember
  • BogdanBogdan Palo Alto, CAMember

    If I may add a question, please :

    after running MUTECT2 in TUMOR-ONLY mode, would it be a good practice to intersect the list of variants with 50-60 GERMLINE VCF files (that we have from other patients), in order to exclude as many germline variants as possible ?

  • shleeshlee CambridgeMember, Administrator, Broadie, Moderator admin

    @Bogdan, presumably, your use of a PoN or known variants resources in your Mutect2 workflow will have already excluded germline variants.

  • BogdanBogdan Palo Alto, CAMember

    Thank you. Please, when you have a minute, could I have the links to the webpages/information that describe the workflow, that describe the use of PoN and the exclusion of germline variants. Thanks ;)

  • shleeshlee CambridgeMember, Administrator, Broadie, Moderator admin

    Hi @Bogdan,

    I've attached a PDF of the original GATK3-MuTect2 hands-on tutorial worksheet that I wrote back in January/February and that was presented by others in Leuven, Belgium (also back in February). Although the attached tutorial is about the previous implementation of M2, and does not use GATK4-M2, the concepts it discusses are still germane. The updated hands-on tutorial that uses GATK4-Mutect2 is written by another teammate. We can expect the team to post the recent UK workshop materials in the blog very shortly as the workshop ended yesterday.

  • BogdanBogdan Palo Alto, CAMember

    many many thanks, the document is very very helpful ;)

  • BogdanBogdan Palo Alto, CAMember

    Dear Lee, please, if I may add another question, namely where I could find a resource that would detail on how to do the selection of somatic variants that were obtained with MUTECT2 run in TUMOR-only mode. Thank you very much ..

  • BogdanBogdan Palo Alto, CAMember

    many many thanks ;)

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