Visual analysis of VCF files

01 January 1970 1 9K Report

I created this R package to allow easy VCF files visual analysis, investigate mutation rates per chromosome, gene, and much more: https://github.com/cccnrc/plot-VCF

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

variant Manhattan-style plots: visualize all/specific variants in your VCF file. You can plot subgroups based on position, sample, gene and/or exon

chromosome summary plots: visualize plot of variants distribution across (selectable) chromosomes in your VCF file

gene summary plots: visualize plot of variants distribution across (selectable) genes in your VCF file

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 on the GitHub page: https://github.com/cccnrc/plot-VCF

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

Widya Pintaka Bayu Putra

I use TASSEL software for genome analysis. You need plink format of map and pad to operate it. You can try and explore this software

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