DOI: 10.18129/B9.bioc.VariantFiltering  

Filtering of coding and non-coding genetic variants

Bioconductor version: Release (3.17)

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>

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biocViews Annotation, Genetics, HighThroughputSequencing, Homo_sapiens, SNP, Sequencing, Software
Version 1.36.1
In Bioconductor since BioC 2.14 (R-3.1) (9.5 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
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
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