Bioconductor – genotypeeval

DOI: 10.18129/B9.bioc.genotypeeval  

 

This package is for version 3.10 of Bioconductor;
for the stable, up-to-date release version, see
genotypeeval.

QA/QC of a gVCF or VCF file

Bioconductor version: 3.10

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
“3.6”) and enter:

if (!requireNamespace("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 1.18.0
In Bioconductor since BioC 3.2 (R-3.2) (4.5 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
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