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Is it too early to be publishing data analysed by MuTect2?

djmarshdjmarsh Sydney, AustraliaMember

Is it too early to be publishing data analysed by MuTect2 in a comparative sense with Haplotype Caller? Is it still strictly in testing phase?

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Best Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MA admin
    Accepted Answer
    Oh I see. No, HaplotypeCaller is completely unsuitable for somatice variant discovery; among other things the genotyping model is simply not appropriate as it makes ploidy assumptions that are not satisfied in a somatic context. You're more than welcome to publish a comparison making this point explicitly, as it would be a public service to demonstrate to others that using HC for somatic analysis does not work well and is not recommended.

Answers

  • djmarshdjmarsh Sydney, AustraliaMember

    Thank you for your response. In a "comparative" sense meaning that we have a dataset from a tumor cohort (so somatic mutations) that was analysed with Haplotype Caller. MuTect2 analyses now showing a lot more very low frequency variants in our GOI not found with Haplotype Caller (I realise more suitable for germline, but I think many have used for somatic too?). We haven't tried just MuTect. Your thoughts on this are appreciated.

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin
    Accepted Answer
    Oh I see. No, HaplotypeCaller is completely unsuitable for somatice variant discovery; among other things the genotyping model is simply not appropriate as it makes ploidy assumptions that are not satisfied in a somatic context. You're more than welcome to publish a comparison making this point explicitly, as it would be a public service to demonstrate to others that using HC for somatic analysis does not work well and is not recommended.
  • djmarshdjmarsh Sydney, AustraliaMember

    Thank you - very helpful.

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