How to calculate TMB for somatic data TCGA

Question

[NT]

Hi, I have to calculate for the first time the tumor mutational burden (TMB) for each sample of a big maf file of TCGA (https://gdc.cancer.gov/about-data/publications/mc3-2017) (the maf file), I'm a beginner on bioinformatic and coding and I didn't find any tool that allows me to calculate TMB for each sample. Does anyone know a tool for TMB calculation or can told me how can i do it for each sample?

Thank u and 'm sorry if my question is a silly question...

[sviatoslav.kendall]

Count the number of somatic mutations in each sample then divide that number by the length of the sequencing panel used (in megabases). If they were all sequenced using the same protocol, you can probably get away with just counting the number of somatic mutations. If your MAF file contains all the samples you're interested in, you can probably just count the number of times each sample appears in the file.

Answer 1

[Kevin Blighe]

Hey Defne, as you can infer from the comment by sviatoslav.kendall, 'Tumour Mutation Burden' is somewhat a general term, with no strict definition. You can technically calculate TMB using any metric / method that makes intuitive sense, as emphasised by these previous answers on Biostars:

• A: TMB Tumor Mutation Burden
• C: How to calculate Tumor Mutation Burden (TMB) for TCGA samples
• A: Tool or R package for computing Tumor Mutational Burden?

Kevin