VariantAnnotation statistics

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Citations per year

Number of citations per year for the bioinformatics software tool VariantAnnotation
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Tool usage distribution map

This map represents all the scientific publications referring to VariantAnnotation per scientific context
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Associated diseases

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Popular tool citations

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Protocols

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


No version available

Documentation


Maintainer


  • person_outline Valerie Obenchain

Publication for VariantAnnotation

VariantAnnotation citations

 (12)
library_books

Using regulatory genomics data to interpret the function of disease variants and prioritise genes from expression studies

2018
F1000Res
PMCID: 5850119
PMID: 29568492
DOI: 10.5256/f1000research.14748.r30355

[…] q2", "GenomicFeatures", "GenomicInteractions", "GenomicRanges", "ggplot2", "Gviz", "gwascat", "InteractionSet", "recount", "pheatmap", "RColorBrewer", "rtracklayer", "R.utils", "splitstackshape", "VariantAnnotation")) […]

library_books

Forward genetics screen coupled with whole genome resequencing identifies novel gene targets for improving heterologous enzyme production in Aspergillus niger

2018
Appl Microbiol Biotechnol
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. ), BreakDance […]

library_books

Gene expression allelic imbalance in ovine brown adipose tissue impacts energy homeostasis

2017
PLoS One
PMCID: 5493397
PMID: 28665992
DOI: 10.1371/journal.pone.0180378

[…] um 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 and th […]

library_books

A cross package Bioconductor workflow for analysing methylation array data

2017
F1000Res
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 ## [ […]

library_books

The fire ant social chromosome supergene variant Sb shows low diversity but high divergence from SB

2017
Mol Ecol
PMCID: 5485014
PMID: 28220980
DOI: 10.1111/mec.14054

[…] Using a custom r script (version 3.0.2; R Core Team ) with bioconductor packages (Gentleman et al. ) including genomicranges, variantannotation and genomicfeatures, we divided the genome into overlapping sliding windows and estimated different measures of divergence and diversity. To define a sliding window of a given size, […]

library_books

BaalChIP: Bayesian analysis of allele specific transcription factor binding in cancer genomes

2017
Genome Biol
PMCID: 5326502
PMID: 28235418
DOI: 10.1186/s13059-017-1165-7

[…] To annotate ASB SNPs with respect to gene annotations (5 ′ untranslated region, 3 ′ untranslated region, promoter, splice site, coding, intron, or intergenic), we used the VariantAnnotation package (version 1.8.13) in R. To obtain the list of known genes and coordinates, we used known gene annotations from the UCSC genome browser obtained from the TxDb.Hsapiens.UCSC.hg1 […]


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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).

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