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: 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>

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

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

Reference Manual PDF

Details

biocViews BatchEffect, DataImport, Genetics, SNP, Sequencing, Software, VariantAnnotation
Version 1.31.1
In Bioconductor since BioC 3.2 (R-3.2) (8.5 years)
License file LICENSE
Depends R (>= 3.4.0), VariantAnnotation
Imports ggplot2, rtracklayer, BiocGenerics, GenomicRanges, GenomeInfoDb, IRanges, methods, BiocParallel, graphics, stats
System Requirements
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Suggests rmarkdown, testthat, SNPlocs.Hsapiens.dbSNP141.GRCh38, TxDb.Hsapiens.UCSC.hg38.knownGene
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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/
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Old Source Packages for BioC 3.17 Source Archive