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This is the development version of VariantFiltering; for the stable release version, see VariantFiltering.

Filtering of coding and non-coding genetic variants

Bioconductor version: Development (3.19)

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], Joan Fernandez [ctb]

Maintainer: Robert Castelo <robert.castelo at upf.edu>

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


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


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

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


biocViews Annotation, Genetics, HighThroughputSequencing, Homo_sapiens, SNP, Sequencing, Software
Version 1.39.0
In Bioconductor since BioC 2.14 (R-3.1) (10 years)
License Artistic-2.0
Depends R (>= 3.5.0), methods, BiocGenerics(>= 0.25.1), VariantAnnotation(>= 1.13.29)
Imports utils, stats, 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, GenomicScores(>= 1.0.0), Gviz, shiny, shinythemes, shinyjs, DT, shinyTree
System Requirements
URL https://github.com/rcastelo/VariantFiltering
Bug Reports https://github.com/rcastelo/VariantFiltering/issues
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Suggests RUnit, BiocStyle, org.Hs.eg.db, 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
Linking To S4Vectors, IRanges, XVector, Biostrings
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Follow Installation instructions to use this package in your R session.

Source Package VariantFiltering_1.39.0.tar.gz
Windows Binary VariantFiltering_1.39.0.zip (64-bit only)
macOS Binary (x86_64) VariantFiltering_1.39.0.tgz
macOS Binary (arm64) VariantFiltering_1.39.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/VariantFiltering
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/VariantFiltering
Bioc Package Browser https://code.bioconductor.org/browse/VariantFiltering/
Package Short Url https://bioconductor.org/packages/VariantFiltering/
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