About the coverage file

Is the coverage_file necessary in Mutect analysis?
How to get the file?
Thanks.

Best Answer

Answers

  • sicottesicotte Member

    What if we did not use Mutect and have to create our own?
    Are the following mutations to be considered "null"? or just like missense.

    In_Frame_Del DEL
    In_Frame_Ins INS

    Nonsense_Mutation TNP (early stop codon)
    Nonstop_Mutation SNP (invalidated stop codon)

    Splice_Site DNP
    Splice_Site SNP

    Translation_Start_Site DNP
    Translation_Start_Site SNP

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @sicotte
    Hi,

    What exactly are you trying to do? If you are using MuTect2 in GATK3 or Mutect2 in GATK4 (recommended), you do not need a coverage file.

    -Sheila

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