How to merge multiple MAF files (Mutation Annotation Format) into a single MAF file? How to create sample/Tumor_Sample_Barcode in MAF ?
0
0
Entering edit mode
3.4 years ago
mekumi0412 • 0

Hi! I am new to cancer genome. I would like to apply maftools to analysis MAF files. The required input files: (1) an MAF file - can be gz compressed. Required. (2) an optional but recommended clinical data associated with each sample/Tumor_Sample_Barcode in MAF. (3) an optional copy number data if available. Can be GISTIC output or a custom table containing sample names, gene names and copy-number status (Amp or Del). Before processing with maftools, we need to merge MAFs from all samples into a single MAF. My questions are (a). how to merge multiple MAF files into a single MAF file. (b) How to create sample/Tumor_Sample_Barcode in MAF?

I would appreciate if someone can guide me to conduct significant somatic mutation variants analysis. Many thanks!

next-gen • 3.4k views
ADD COMMENT
0
Entering edit mode

Which data have you already got? It's possible to start from the MAF files (can be downloaded from the GDC Legacy Archive). To make things easier, you could instead download data from cBioPortal.

ADD REPLY
0
Entering edit mode

Hi !

I have trying to do something similar. Was wondering if you were able to create the MAF files ?

Any help would be really appreciated. Thanks !

ADD REPLY
0
Entering edit mode

I have trying to do something similar.

It is no good saying this... It gives no indication about the data that you already have right now. So, nobody can help you until you provide more information.

Note that mekumi0412, who posted the original question, has not logged in for > 1 year. His/her post was also lacking in key details.

ADD REPLY

Login before adding your answer.

Traffic: 2298 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6