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. 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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("RareVariantVis")
AuthorAdam Gudys and Tomasz Stokowy
Bioconductor views GenomicVariation Sequencing WholeGenome
Date of publicationNone
MaintainerTomasz Stokowy <tomasz.stokowy@k2.uib.no>
LicenseArtistic-2.0
Version2.2.0

View on Bioconductor

Files

DESCRIPTION
NAMESPACE
R
R/callHomozygous.R R/chromosomeVis.R R/movingAverage.R R/multipleVis.R R/rareVariantVis.R
build
build/vignette.rds
inst
inst/CITATION
inst/doc
inst/doc/RareVariantsVis.R
inst/doc/RareVariantsVis.Rnw
inst/doc/RareVariantsVis.pdf
inst/extdata
inst/extdata/All_20160601_chr19_9-10.vcf.recode.vcf.gz
inst/extdata/All_20160601_chr19_9-10.vcf.recode.vcf.gz.tbi
inst/extdata/CentromeresHg19.txt
inst/extdata/CoriellIndex_S1.sv.vcf.gz
inst/extdata/CoriellIndex_S1.sv.vcf.gz.tbi
inst/extdata/CoriellIndex_S1_chr19_9-10_S1.vcf.recode.vcf.gz
inst/extdata/CoriellIndex_S1_chr19_9-10_S1.vcf.recode.vcf.gz.tbi
inst/extdata/ExAC.r0.3.1.sites.vep_chr19_9-10.vcf.recode.vcf.gz
inst/extdata/ExAC.r0.3.1.sites.vep_chr19_9-10.vcf.recode.vcf.gz.tbi
inst/extdata/RareVariants_CoriellIndex_S1.txt
inst/extdata/RareVariants_Coriell_S2.txt
inst/extdata/RareVariants_Coriell_S3.txt
inst/extdata/StructuralVariants_CoriellIndex_S1.txt
inst/extdata/StructuralVariants_Coriell_S2.txt
inst/extdata/StructuralVariants_Coriell_S3.txt
inst/extdata/UCSC_hg19_chr9_9-10_refSeq_160702.txt
inst/extdata/nexterarapidcapture_exome_targetedregions_v1.2_chr19_9-10.bed
inst/extdata/uniprot-all_chr19_9-10.txt
man
man/callHomozygous.Rd man/chromosomeVis.Rd man/movingAverage.Rd man/multipleVis.Rd man/rareVariantVis.Rd
tests
vignettes
vignettes/CoriellIndex_S1_chr19.png
vignettes/RareVariantsVis.Rnw
vignettes/interactive.png

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