genotypeeval

DOI: 10.18129/B9.bioc.genotypeeval    

QA/QC of a gVCF or VCF file

Bioconductor version: Release (3.8)

Takes in a gVCF or VCF and reports metrics to assess quality of calls.

Author: Jennifer Tom [aut, cre]

Maintainer: Jennifer Tom <tom.jennifer at gene.com>

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

Installation

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

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("genotypeeval", version = "3.8")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("genotypeeval")

 

HTML genotypeeval_vignette.html
PDF   Reference Manual
Text   NEWS
Text   LICENSE

Details

biocViews BatchEffect, DataImport, Genetics, SNP, Sequencing, Software, VariantAnnotation
Version 1.14.0
In Bioconductor since BioC 3.2 (R-3.2) (3 years)
License file LICENSE
Depends R (>= 3.4.0), VariantAnnotation
Imports ggplot2, rtracklayer, BiocGenerics, GenomicRanges, GenomeInfoDb, IRanges, methods, BiocParallel, graphics, stats
LinkingTo
Suggests rmarkdown, testthat, SNPlocs.Hsapiens.dbSNP141.GRCh38, TxDb.Hsapiens.UCSC.hg38.knownGene
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package genotypeeval_1.14.0.tar.gz
Windows Binary genotypeeval_1.14.0.zip
Mac OS X 10.11 (El Capitan) genotypeeval_1.14.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/genotypeeval
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/genotypeeval
Package Short Url http://bioconductor.org/packages/genotypeeval/
Package Downloads Report Download Stats

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