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Mutect for Rat data

chris2015chris2015 USMember

I would like to confirm that when i use mutect with Rat data, it is not necessary to add neither dbsnp file nor COSMIC file (As COSMIC data is for human cancer only).
What about if i provided only dpsnp file, any call that is in dpsnp file will be excluded wether it is germ or somatic snp??

Thank you.

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  • chris2015chris2015 USMember

    Thank you very much for reply.
    So, all mutect calls that are in dpsnp file will be excluded??

    Issue · Github
    by Sheila

    Issue Number
    280
    State
    open
    Last Updated
  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    I believe so, unless they are also in COSMIC, in which case they get whitelisted.

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi there, we got some additional details and a slight correction from the MuTect developers:

    The dbSNP information isn't directly used to filter out mutations, but rather increase the threshold for calling it somatic (increasing the prior of it being non-somatic). We don't currently inspect any information in the dbsnp track because we generally don't trust it for somatic.

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