I created this R package to allow easy VCF files visual analysis, investigate mutation rates per chromosome, gene, and much more: plotVCF

The package is divided into 3 main sections, based on analysis target:

1. Manhattan-style plots: visualize all/specific variants in your VCF file. You can plot subgroups based on position, sample, gene and/or exon (createVCFplot())
2. chromosome summary plots: visualize plot of variants distribution across (selectable) chromosomes in your VCF file (chrAnalysis())
3. gene summary plots: visualize plot of variants distribution across (selectable) genes in your VCF file (geneAnalysis())

Take a look at how many different things you can achieve in just one line of code! It is extremely easy to install and use, well documented (I hope) on the GitHub page.

As example, you can plot variants based on user-defined flags:

Or analyze gene-distribution of you variants: And much much more. Find it our here!

I'd love to have your opinion, idea, comment, suggestion, bugs you might find, etc.