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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>

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PDF R Script RareVariantVis
PDF   Reference Manual


biocViews GenomicVariation, Sequencing, Software, WholeGenome
Version 2.2.0
In Bioconductor since BioC 3.2 (R-3.2) (1.5 years)
License Artistic-2.0
Depends BiocGenerics, VariantAnnotation, googleVis, GenomicFeatures
Imports S4Vectors, IRanges, GenomeInfoDb, GenomicRanges, gtools, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, phastCons100way.UCSC.hg19, SummarizedExperiment, GenomicScores
Suggests knitr
Depends On Me
Imports Me
Suggests Me
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