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MuTect algorithm

Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin
edited August 2014 in MuTect v1
This discussion was created from comments split from: MuTect source now available in GitHub!.
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Comments

  • turbowturbow TokyoMember

    I am using MuTect for detecting mutations of cancer samples.
    And for further understanding, I would like to calculate the algorithm of MuTect on my own.
    Then I have one question about "Variant detection". There is a score called "LODT", and how can I calculate the value "P(m,f)"?
    Is this same as "f"? I couldn't understand about this factor.
    Any support will be appreciated.
    Thanks.

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    @turbow‌ I'm sorry, I don't understand your question. Can you please clarify what you mean by "calculate the algorithm of MuTect on my own"? Are you trying to follow the math explained in the MuTect paper?

  • turbowturbow TokyoMember

    @Geraldine_VdAuwera‌ I'm sorry about my poor English. Yes, I want to follow the math explained in the MuTect paper using my sample datasets to clarify the algorithm and know what is going on in the "Variant detection" phase.

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Oh I see, thank you for clarifying. Unfortunately we're not currently able to provide that level of information. If you want details beyond what is in the paper, you will need to step through the code, which is freely accessible on Github.

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