mutect wig.txt file

How is the wiggle file from music created? Does 0 imply no coverage in either normal or tumor while 1 implies reads present in both?
Without calling mutations, is there a way to create just the wig.txt files if I have the tumor/normal bams.

Thank you,
Teja

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  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    Hi Teja,

    I believe your interpretation is correct, that 0 implies no coverage in either normal or tumor while 1 implies reads present in both. There is no way to get just the coverage and not the calls with MuTect, but GATK offers some coverage analysis tools if that's what you are interested in.

  • Hi Geraldine,
    I am still preparing files etc for using mutect this is my first time with this tool) and one silly question about the wiggle file, it is an output or an input file?

    When reading the indications about how to run Mutect i thought that it was an input i must to prepare (using bed tools etc)
    but now reading these comments, i think i was wrong interpreting the indications and that the wig file is just an output file so i do no need to prepare it for running mutect. Is that so?

    thank you in advance

    carlx

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    The wiggle file is an optional output created by MuTect, you don't need to prepare it.

  • Is the wig file the coverage in the tumor, normal, or both combined?

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