Extracting mutation status from MAF files - TCGA

Question

[yahn]

Hello, I would like to ask how to extract mutation status from MAF files on the TCGA website. I downloaded MuTect2 annotated somatic mutation, with the format of MAF. As shown on the TCGA website, there are different columns in the file.

However, as these MAF files only contains mutated genes (IND, DEL, SNP...), I am not sure how I can identify WT genes for each patient. The resulting data frame I would like to have is a matrix of WT, and MUT with patient ID as row index and gene names as column names.

[Thanujay S]

Hey! Can you explain the question further? What have you tried?

[Zhenyu Zhang]

you can assume all genes without mutation is WT (easy) while controlling for (difficult)

• coverage
• capture region
• germline
• the particular filtering schema your MAF has been processed

So in short, you can easily get what you want, but very difficult to get it correct.