Test-drive the GATK tools and Best Practices pipelines on Terra


Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

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

Sign In or Register to comment.