VariantAnnotation

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see VariantAnnotation.

Annotation of Genetic Variants

Bioconductor version: 3.8

Annotate variants, compute amino acid coding changes, predict coding outcomes.

Author: Valerie Obenchain [aut, cre], Martin Morgan [aut], Michael Lawrence [aut], Stephanie Gogarten [ctb]

Maintainer: Valerie Obenchain <maintainer at bioconductor.org>

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

To install this package, start R (version "3.5") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
BiocManager::install("VariantAnnotation")

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:

browseVignettes("VariantAnnotation")

1. Introduction to VariantAnnotation PDF R Script

2. Using filterVcf to Select Variants from VCF Files PDF R Script

Reference Manual PDF

NEWS Text

Reading VCF data Video

Version 1.28.13

In Bioconductor since BioC 2.9 (R-2.14) (12.5 years)

License Artistic-2.0

Depends R (>= 2.8.0), methods, BiocGenerics(>= 0.15.3), GenomeInfoDb(>= 1.15.2), GenomicRanges(>= 1.31.8), SummarizedExperiment(>= 1.9.9), Rsamtools(>= 1.33.6)

Imports utils, DBI, zlibbioc, Biobase, S4Vectors(>= 0.17.24), IRanges(>= 2.13.13), XVector(>= 0.19.7), Biostrings(>= 2.47.6), AnnotationDbi(>= 1.27.9), rtracklayer(>= 1.39.7), BSgenome(>= 1.47.3), GenomicFeatures(>= 1.31.3)

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

Mac OS X 10.11 (El Capitan) VariantAnnotation_1.28.13.tgz

Source Repository git clone https://git.bioconductor.org/packages/VariantAnnotation

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/VariantAnnotation

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