RareVariantVis - A suite for analysis of rare genomic variants in whole genome
sequencing data
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. For
discovered rare variants CRISPR guide RNAs are designed, so the
user can plan further functional studies. 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.