Variant analysis for mouse WES

Question

[alba]

Hi all,

I’m working with mouse WES data and have a set of VCFs that I’d like to analyze using a package similar to maftools. Ideally, I’m looking for something user-friendly that works with mouse genome assemblies.

I don’t mind which programming language the tool is implemented in, as long as it can handle mouse data. So far, I haven’t been able to find a package that fits these criteria. Any suggestions would be greatly appreciated.

Thanks in advance! Alba

[GenoMax]

I’d like to analyze using a package similar to maftools.

Looks like maftools works with mouse data: https://github.com/PoisonAlien/maftools/issues/197 Are you thinking it does not or are you looking for a different package.

[alba]

I saw that but it looks like it only works for trinucleotideMatrix() specifically, I was looking to be able to generate rainfallPlot(), for example...

[GenoMax]

You could open a new issue and ask the developers of maftools if this was something they can add.

[barslmn]

You can try Ensembl VEP which can also annotate organism other than human.

[alba]

Hi, thanks for the suggestion! I’m aware of Ensembl VEP, and in fact, I already have my VCFs annotated with VEP. The challenge I’m facing is that VEP annotations can be a bit messy to work through, especially when filtering out non-canonical annotations or variants.

What I was looking for is something more user-friendly for quick downstream analysis. I’m comfortable working with VCFs in Python, but it often turns into a lot of manual filtering and parsing. That’s why I thought of maftools, it does a really nice job of summarizing the variants and their functional annotations, but unfortunately it doesn’t seem to support mm10/mouse genomes (with the exception of just a couple of functions).