How can I get the corresponding protein sequence according to the MAF file？

Question

[LeeLee]

Hi,

I downloaded a file in MAF format from TCGA, and I want to get the sequence of the corresponding mutant protein from this file (if the mutation occurs in the CDS and changes the corresponding amino acid), are there any good tools that can help me achieve this?

Thanks， LeeLee

[Hamid Ghaedi]

This seems a very specific situation and I haven't heard about such a function, but having a list of mutations and gene/protein sequences you can do this job. If you gave that a try and faced difficulty, you may post errors here to get help.

Answer 1

[Jeremy]

There's an R package called maftools that might be helpful, although I'm afraid I'm not familiar with it myself.