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How can MutSigCV be applied to germline mutation driver gene discovery?

Hi,
we only have snp data(vcf format) from normal sample of the normal people without paired tumor sample. I have translated the vcf format data to the MAF data(any info about tumor sample were set null or unknown, while the normal sample info (Matched_Norm_Sample_Barcode) were set as patient id). However, when I run the Mutsig, it came out the error: MutSig is not applicable to single patients. However, my data do from multiple patient. What would be the problem? By the way, the log also has following NOTE: 1064544/1064680 mutations were outside the category set. Excluding them. Is the problem came from the format of the transformed MAF? Do I need to place the Matched_Norm_Sample_Barcode to the Tumor_Sample_Barcode or do I need to do other things? Thanks!

Best Answer

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi there, sorry for the late reply. I'm not sure I understand what you are trying to do; this doesn't sound like the supported use case for MutSig CV. Perhaps if you clarify what you are trying to do, I can suggest an appropriate method.

  • cindylanzaocindylanzao ShenzhengMember

    Thanks Geraldine, the thing I want to do is trying to identify the driver genes with germline mutations.

  • HasaniHasani GermanyMember
    edited February 2016

    I'm trying to wrap my head around the valid value of the "categ" column. Could you please further help?
    I'm wondering what is the point of having column "categ" if I have the column Variant_Classification according to Sequence Ontology? Besides, how can I say if intron_variant is null, noncoding, or silent?

    Thanks!

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Sorry, we're not able to provide support for MutSig at this time.

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