To install this package, start R and enter:

## try http:// if https:// URLs are not supported

In most cases, you don't need to download the package archive at all.


DOI: 10.18129/B9.bioc.VariantFiltering    

Filtering of coding and non-coding genetic variants

Bioconductor version: Release (3.5)

Filter genetic variants using different criteria such as inheritance model, amino acid change consequence, minor allele frequencies across human populations, splice site strength, conservation, etc.

Author: Robert Castelo [aut, cre], Dei Martinez Elurbe [ctb], Pau Puigdevall [ctb]

Maintainer: Robert Castelo <robert.castelo at>

Citation (from within R, enter citation("VariantFiltering")):


To install this package, start R and enter:

## try http:// if https:// URLs are not supported


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



PDF R Script VariantFiltering: filter coding and non-coding genetic variants
PDF   Reference Manual
Text   NEWS


biocViews Annotation, Genetics, HighThroughputSequencing, Homo_sapiens, SNP, Sequencing, Software
Version 1.12.2
In Bioconductor since BioC 2.14 (R-3.1) (3.5 years)
License Artistic-2.0
Depends R (>= 3.0.0), methods, BiocGenerics(>= 0.13.8), VariantAnnotation(>= 1.13.29)
Imports utils, DBI, RSQLite (>= 1.0.0), Biobase, S4Vectors(>= 0.9.25), IRanges(>= 2.3.23), RBGL, graph, AnnotationDbi, BiocParallel, Biostrings(>= 2.33.11), GenomeInfoDb(>= 1.3.6), GenomicRanges(>= 1.19.13), SummarizedExperiment, GenomicFeatures, Rsamtools(>= 1.17.8), BSgenome, Gviz, shiny, GenomicScores
LinkingTo S4Vectors, IRanges, XVector, Biostrings
Suggests RUnit, BiocStyle,, BSgenome.Hsapiens.1000genomes.hs37d5, TxDb.Hsapiens.UCSC.hg19.knownGene, SNPlocs.Hsapiens.dbSNP144.GRCh37, MafDb.1Kgenomes.phase1.hs37d5, phastCons100way.UCSC.hg19, PolyPhen.Hsapiens.dbSNP131, SIFT.Hsapiens.dbSNP137
Depends On Me MafDb.1Kgenomes.phase1.hs37d5, MafDb.1Kgenomes.phase3.hs37d5, MafDb.ESP6500SI.V2.SSA137.GRCh38, MafDb.ESP6500SI.V2.SSA137.hs37d5, MafDb.ExAC.r0.3.1.snvs.hs37d5, MafDb.ExAC.r1.0.hs37d5, MafDb.ExAC.r1.0.nonTCGA.hs37d5, MafDb.gnomAD.r2.0.1.hs37d5, MafDb.gnomADex.r2.0.1.hs37d5
Imports Me
Suggests Me
Build Report  

Package Archives

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

Source Package VariantFiltering_1.12.2.tar.gz
Windows Binary (32- & 64-bit)
Mac OS X 10.11 (El Capitan) VariantFiltering_1.12.2.tgz
Source Repository git clone
Package Short Url
Package Downloads Report Download Stats

Documentation »


R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: