genotypeeval

DOI: 10.18129/B9.bioc.genotypeeval    

This is the development version of genotypeeval; for the stable release version, see genotypeeval.

QA/QC of a gVCF or VCF file

Bioconductor version: Development (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")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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	1.31.0
In Bioconductor since	BioC 3.2 (R-3.2) (7 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
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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)
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