genotypeeval

DOI: 10.18129/B9.bioc.genotypeeval  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see genotypeeval.

QA/QC of a gVCF or VCF file

Bioconductor version: 3.16

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>

Installation

To install this package, start R (version "4.2") and enter:

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

BiocManager::install("genotypeeval")

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	1.30.0
In Bioconductor since	BioC 3.2 (R-3.2) (7.5 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_1.30.0.tar.gz
Windows Binary	genotypeeval_1.30.0.zip (64-bit only)
macOS Binary (x86_64)	genotypeeval_1.29.0.tgz
macOS Binary (arm64)	genotypeeval_1.30.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/genotypeeval
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/genotypeeval
Bioc Package Browser	https://code.bioconductor.org/browse/genotypeeval/
Package Short Url	https://bioconductor.org/packages/genotypeeval/
Package Downloads Report	Download Stats