How to find differentially mutated genes between two groups of samples?

Question

[7829453]

I am currently trying to analyze whole genome sequencing data in lung cancer and have split the samples (80 in total) into 2 groups - those with doubled genomes and those without. I would like to see what genes are disproportionately mutated in the doubled genome samples compared to the non-doubled genome samples (and vice versa). I have the mutations for each sample in MAF format. Is there a package that can easily perform this type of analysis? If not, how should I approach this?

Answer 1

[sbstevenlee]

You could use the pymaf submodule from the fuc package I wrote. More specifically, you can create an oncoplot to simultaneously display frequent gene mutations and annotations of interest (e.g. genome duplication) as shown below:

Above example is from: https://sbslee-fuc.readthedocs.io/en/latest/tutorials.html#create-customized-oncoplots