Somatic mutations per gene

Question

[zephyr_falcon]

Hi,

I have a vcf file (from Mutect2) - list of somatic mutations and their genomic locations & other info.

Does anyone know that there is a R package that can calculate the number of somatic mutations per gene?

For example, map the somatic mutations in the vcf file to any one gene based on their location and count how many mutations in each gene?

I can do it myself manually, but if there's a package that can do that, I can save time.

Thanks..

[shawn.w.foley]

As far as counting, I don't know of any, but snpEff can annotate SNPs, mapping them to genes and qualifying them as "HIGH", "MEDIUM", or "LOW" severity. You can then filter for SNPs that are meaningful to your project.

From there you could load the data into R, convert the gene data into a factor, then run the summary command to count the instances of each gene.

[zephyr_falcon]

Yes, I can annotate the mutations using VEP (https://useast.ensembl.org/info/docs/tools/vep/index.html), and then count them per gene on my own.

But I just wondered if there's a tool to do all of them automatically.

Thanks for your comment anyway.

Answer 1

[Alewa]

@zephyr_falcon maybe Maftools the R package could be useful (i could be wrong though); https://bioconductor.org/packages/release/bioc/html/maftools.html

Maftools accepts a standard .maf file as input but there is a way to convert vcf2maf; https://bioconductor.org/packages/release/bioc/vignettes/maftools/inst/doc/maftools.html#2_generating_maf_files