VariantAnnotation protocols

View VariantAnnotation computational protocol

VariantAnnotation statistics

To access cutting-edge analytics on consensus tools, life science contexts and associated fields, you will need to subscribe to our premium service.

Subscribe
info

Citations per year

Citations chart
info

Popular tool citations

chevron_left SNP/SNV annotation chevron_right
Popular tools chart
info

Tool usage distribution map

Tool usage distribution map
info

Associated diseases

Associated diseases

VariantAnnotation specifications

Information


Unique identifier OMICS_02073
Name VariantAnnotation
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License Artistic License version 2.0
Computer skills Advanced
Version 1.26.1
Stability Stable
Requirements
methods, Biobase, utils, BiocStyle, zlibbioc, ggplot2, BSgenome.Hsapiens.UCSC.hg19, RUnit, BSgenome(>=1.47.3), snpStats, R(>=2.8.0), DBI, BiocGenerics(>=0.15.3), Biostrings(>=2.47.6), GenomicRanges(>=1.31.8), TxDb.Hsapiens.UCSC.hg19.knownGene, GenomeInfoDb(>=1.15.2), AnnotationHub, SummarizedExperiment(>=1.9.9), Rsamtools(>=1.31.2), S4Vectors(>=0.17.24), IRanges(>=2.13.13), XVector(>=0.19.7), AnnotationDbi(>=1.27.9), rtracklayer(>=1.39.7), GenomicFeatures(>=1.31.3), SNPlocs.Hsapiens.dbSNP.20101109, SIFT.Hsapiens.dbSNP132, SIFT.Hsapiens.dbSNP137, PolyPhen.Hsapiens.dbSNP131
Maintained Yes

Taxon


  • Primates
    • Homo sapiens

Versioning


Add your version

Documentation


Maintainer


  • person_outline Valerie Obenchain <>

Publication for VariantAnnotation

VariantAnnotation in pipelines

 (5)
2018
PMCID: 5850119
PMID: 29568492
DOI: 10.5256/f1000research.14748.r30355

[…] "genomicfeatures", "genomicinteractions", "genomicranges", "ggplot2", "gviz", "gwascat", "interactionset", "recount", "pheatmap", "rcolorbrewer", "rtracklayer", "r.utils", "splitstackshape", "variantannotation")) , we start with a common scenario: we ran a rna-seq experiment comparing patients with a disease and healthy individuals, and would like to discover key disease genes […]

2018
PMCID: 5895441
PMID: 29651456
DOI: 10.1126/sciadv.1701799

[…] of each variant group were then compared using two-sample t tests assuming binomial variances (, a and b)., exome variants were mapped to amino acid changes in the target protein using bioconductor variantannotation package (). 1d linear protein domain structures were visualized using cbioportal mutationmapper (). protein domain data were retrieved from the pfam database () and updated […]

2017
PMCID: 4916993
PMID: 27347385
DOI: 10.5256/f1000research.9514.r14245

[…] [44] xml_3.98-1.5 ## [45] beanplot_1.2 ## [46] org.hs.eg.db_3.4.0 ## [47] annotationhub_2.6.5 ## [48] zlibbioc_1.20.0 ## [49] mass_7.3-45 ## [50] scales_0.4.1 ## [51] bsgenome_1.42.0 ## [52] variantannotation_1.20.3 ## [53] biocinstaller_1.24.0 ## [54] geoquery_2.40.0 ## [55] yaml_2.1.14 ## [56] memoise_1.0.0 ## [57] gridextra_2.2.1 ## [58] ggplot2_2.2.1 ## [59] pkgmaker_0.22 ## […]

2016
PMCID: 5114598
PMID: 27834372
DOI: 10.1038/ncomms13390

[…] of the snps are expected to be homozygous. heterozygous snps were considered potential artefacts and removed. snps were categorized as coding, synonymous, nonsynonymous and nonsense using r package variantannotation v1.13.46., core and variable genes were compared with respect to gene length, exon number, coding snp density, synonymous (not resulting in amino-acid change), nonsynonymous […]

2015
PMCID: 4494700
PMID: 26153459
DOI: 10.1186/s12864-015-1700-4

[…] l1 or alu presence (and change the call from “absent” to “present”, see below). unless indicated, analyses were performed in r/bioconductor [, ], including packages shortread [], rtracklayer [] and variantannotation []., the presence of a particular amplicon was associated with a large number of specific reads (as assessed by the genomic alignment of read tags) whereas its absence […]


To access a full list of citations, you will need to upgrade to our premium service.

VariantAnnotation in publications

 (17)
PMCID: 5895441
PMID: 29651456
DOI: 10.1126/sciadv.1701799

[…] of each variant group were then compared using two-sample t tests assuming binomial variances (, a and b)., exome variants were mapped to amino acid changes in the target protein using bioconductor variantannotation package (). 1d linear protein domain structures were visualized using cbioportal mutationmapper (). protein domain data were retrieved from the pfam database () and updated […]

PMCID: 5850119
PMID: 29568492
DOI: 10.5256/f1000research.14748.r30355

[…] "genomicfeatures", "genomicinteractions", "genomicranges", "ggplot2", "gviz", "gwascat", "interactionset", "recount", "pheatmap", "rcolorbrewer", "rtracklayer", "r.utils", "splitstackshape", "variantannotation")) , we start with a common scenario: we ran a rna-seq experiment comparing patients with a disease and healthy individuals, and would like to discover key disease genes […]

PMCID: 5796395
PMID: 29394955
DOI: 10.1186/s40246-018-0136-8

[…] from the 1000 genomes ftp site (ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/), and genotype information from all snps overlapping with the belphg-21 study was extracted using the r variantannotation package []. belgian data were mapped independently on the pc model. the pc analysis was performed using the most informative snps by applying the following filtering criteria: (1) […]

PMCID: 5794824
PMID: 29305699
DOI: 10.1007/s00253-017-8717-3

[…] using gatk genotypegvcfs. variants called by bcftools were filtered using vcftools, and variants called by gatk were filtered using gatk variantfiltration. filtered variants were annotated using the variantannotation package in r (obenchain et al. ). structural variations such as insertion, deletion, or duplication of relatively large segments were identified using pindel (ye et al. ), […]

PMCID: 5493397
PMID: 28665992
DOI: 10.1371/journal.pone.0180378

[…] level of gene expression. the rigorous, progressive filtering reduced the number of informative snps to 24,355 (filtered snps). snp filtering was undertaken using the filtervcf function within the variantannotation r package (version 1.18.6). we considered how varying the minimal coverage threshold per locus impacted the number of filtered snps obtained, the number of genes tested for ai […]


To access a full list of publications, you will need to upgrade to our premium service.

VariantAnnotation institution(s)
Program in Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA; Bioinformatics and Computational Biology, Genentech, South San Francisco, CA, USA; Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA; Department of Biostatistics, University of Washington, Seattle, WA, USA
VariantAnnotation funding source(s)
Supported by National Human Genome Research Institute of the National Institutes of Health (U41HG004059).

VariantAnnotation reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review VariantAnnotation