Question About How To Make Maf File For Music

Question

[Ryo Murasaki]

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

Answer 1

[Chris Miller]

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

[Ryo Murasaki]

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