identify highly mutated regions in WES/WGS samples

Question

[cocchi.e89]

Hi all, I'm wondering if there's any tool available that allows identification of highly mutated regions starting from WES/WGS data. I'm interested in understanding if there are regions that are particularly mutated (respect the normal reference) from a set of my samples and if these "mutational hotspots" are shared across samples.

I generally work more on Diagnsotic data, this is more cancer-related request, but I'm pretty sure that some tool have been created for that, so I hope you experienced users will known it

Thank you very much in advance for any help/recommendation!

Answer 1

[igor]

You can do it with maftools:

Cancer genomes, especially solid tumors are characterized by genomic loci with localized hyper-mutations. Such hyper mutated genomic regions can be visualized by plotting inter variant distance on a linear genomic scale. These plots generally called rainfall plots and we can draw such plots using rainfallPlot. If detectChangePoints is set to TRUE, rainfall plot also highlights regions where potential changes in inter-event distances are located.

[cocchi.e89]

Thanks @igor, it looks like what I was looking for

[cocchi.e89]

@igor, do you need to put only somatic mutations in the input MAF file or both somatic and germline?

[igor]

MAF file can contain any mutations. It's up to the user to determine how to filter the mutations.