genotypeeval

DOI: 10.18129/B9.bioc.genotypeeval  

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This package is for version 3.17 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see genotypeeval.

QA/QC of a gVCF or VCF file

Bioconductor version: Release (3.17)

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 "4.3") 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

PDF		Reference Manual

Details

biocViews	BatchEffect, DataImport, Genetics, SNP, Sequencing, Software, VariantAnnotation
Version	1.31.1
In Bioconductor since	BioC 3.2 (R-3.2) (8 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
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)	genotypeeval_1.31.1.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	https://bioconductor.org/packages/genotypeeval/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.17	Source Archive