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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 (3.0)

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: Dei M. Elurbe, Robert Castelo

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 1.1.9
In Bioconductor since BioC 2.14 (R-3.1)
License Artistic-2.0
Depends R (>= 3.0.0), methods, BiocGenerics(>= 0.11.3)
Imports DBI, RSQLite (>= 0.8-1), Biobase, S4Vectors, IRanges(>= 1.99.17), AnnotationDbi, BiocParallel, Biostrings(>= 2.33.11), GenomeInfoDb(>= 1.1.3), GenomicRanges(>= 1.17.19), Rsamtools(>= 1.17.8), BSgenome, BSgenome.Hsapiens.UCSC.hg19, VariantAnnotation(>= 1.11.4), shiny
Suggests BiocStyle,, TxDb.Hsapiens.UCSC.hg19.knownGene, SNPlocs.Hsapiens.dbSNP.20120608, MafDb.ALL.wgs.phase1.release.v3.20101123, MafDb.ESP6500SI.V2.SSA137.dbSNP138, phastCons100way.UCSC.hg19, PolyPhen.Hsapiens.dbSNP131, SIFT.Hsapiens.dbSNP137
System Requirements
Depends On Me MafDb.ALL.wgs.phase1.release.v3.20101123, MafDb.ALL.wgs.phase1.release.v3.20101123, MafDb.ESP6500SI.V2.SSA137.dbSNP138, MafDb.ESP6500SI.V2.SSA137.dbSNP138, phastCons100way.UCSC.hg19, phastCons100way.UCSC.hg19
Imports Me
Suggests Me

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Package Source VariantFiltering_1.1.9.tar.gz
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Mac OS X 10.6 (Snow Leopard) VariantFiltering_1.1.9.tgz
Mac OS X 10.9 (Mavericks) VariantFiltering_1.1.9.tgz
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