How to calculate base substitution mutation frequency (C>T T>A C>G T>C T>G C>A) from TCGA MAF files

Question

[Mike]

Hi All,
I have TCGA MAF files and want to calculate base substitution mutation frequency (C>T , T>A , C>G , T>C , T>G , C>A) per sample. If anyone knows please help me ?

Thanks

Answer 1

[Martina]

Hello, isn't maftools plotmafSummary what you are looking for? https://www.bioconductor.org/packages/release/bioc/vignettes/maftools/inst/doc/maftools.html