Question: Question About How To Make Maf File For Music
2
gravatar for Ryo Murasaki
6.3 years ago by
Ryo Murasaki30
Japan
Ryo Murasaki30 wrote:

Hi, All

I don't know how to make MAF file for Genome MuSiC. My protocol is below.

  1. Normal Samples Exome Analysis
    (BWA->GATK->Normal Samples' Group Annotation info.)

  2. Tumor Samples Exome Analysis
    (BWA->GATK->Tumor Samples' Group Annotation info.)

  3. Make MAF file
    (Tumor Annotation info.) \ (Normal Annotation info.)
    in other words, the relative complement of Normal Annotation set in Tumor Annotation set

Is this correct? or simply, use only Tumor Annotation info.?

if you know best practice, could you tell me that?

Thank you,

Ryo

music • 1.7k views
ADD COMMENTlink modified 6.3 years ago by Chris Miller20k • written 6.3 years ago by Ryo Murasaki30
3
gravatar for Chris Miller
6.3 years ago by
Chris Miller20k
Washington University in St. Louis, MO
Chris Miller20k wrote:

A MAF file typically consists only of variants predicted to be somatic. This means that they should be present in the tumor, but not the normal (ignoring for the moment low-level tumor contamination in the normal). These tumor-specific variants should be annotated in the MAF file, according to the specifications here: https://wiki.nci.nih.gov/display/TCGA/Mutation+Annotation+Format+(MAF)+Specification

ADD COMMENTlink written 6.3 years ago by Chris Miller20k

Hi, Chris I really appreciate your quick response. Thank you very much.

ADD REPLYlink written 6.3 years ago by Ryo Murasaki30
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