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Filtering of coding and non-coding genetic variants

Bioconductor version: Release (3.1)

Filter genetic variants using different criteria such as inheritance model, amino acid change consequence, minimum 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>

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PDF VariantFiltering: filter coding and non-coding genetic variants
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biocViews Annotation, Genetics, HighThroughputSequencing, Homo_sapiens, SNP, Sequencing, Software
Version 1.4.3
In Bioconductor since BioC 2.14 (R-3.1) (1.5 years)
License Artistic-2.0
Depends R (>= 3.0.0), methods, BiocGenerics(>= 0.13.8), VariantAnnotation(>= 1.13.29)
Imports DBI, RSQLite (>= 1.0.0), Biobase, S4Vectors, IRanges(>= 2.1.18), RBGL, graph, AnnotationDbi, BiocParallel, Biostrings(>= 2.33.11), GenomeInfoDb(>= 1.3.6), GenomicRanges(>= 1.19.13), GenomicFeatures, Rsamtools(>= 1.17.8), BSgenome, Gviz, shiny
LinkingTo S4Vectors, IRanges, XVector, Biostrings
Suggests BiocStyle,, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, SNPlocs.Hsapiens.dbSNP.20120608, MafDb.ALL.wgs.phase1.release.v3.20101123, MafDb.ESP6500SI.V2.SSA137, MafDb.ExAC.r0.3.sites, phastCons100way.UCSC.hg19, PolyPhen.Hsapiens.dbSNP131, SIFT.Hsapiens.dbSNP137
Depends On Me MafDb.ALL.wgs.phase1.release.v3.20101123, MafDb.ALL.wgs.phase3.release.v5a.20130502, MafDb.ESP6500SI.V2.SSA137, MafDb.ExAC.r0.3.sites, phastCons100way.UCSC.hg19, phastCons7way.UCSC.hg38
Imports Me
Suggests Me
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