RareVariantVis

A suite for analysis of rare genomic variants in whole genome sequencing data

Bioconductor version: Release (3.5)

Second version of RareVariantVis package aims to provide comprehensive information about rare variants for your genome data. It annotates, filters and presents genomic variants (especially rare ones) in a global, per chromosome way. Large structural variants, including copy number variants are also supported. Package accepts variants directly from variant caller - for example GATK or Speedseq. Output of package are lists of variants together with adequate visualization. Visualization of variants is performed in two ways - standard that outputs png figures and interactive that uses JavaScript d3 package. Interactive visualization allows to analyze trio/family data, for example in search for causative variants in rare Mendelian diseases, in point-and-click interface. The package includes homozygous region caller and allows to analyse whole human genomes in less than 30 minutes on a desktop computer. RareVariantVis disclosed novel causes of several rare monogenic disorders, including one with non-coding causative variant - keratolythic winter erythema.

Author: Adam Gudys and Tomasz Stokowy

Maintainer: Tomasz Stokowy <tomasz.stokowy at k2.uib.no>

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("RareVariantVis")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("RareVariantVis")

Details

Package Archives

Follow Installation instructions to use this package in your R session.