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

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?

cancer sequencing mutations
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updated by sbstevenlee • sbstevenlee • written by 7829453 • 7829453

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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:

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

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written by sbstevenlee • sbstevenlee

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