genotypeeval

DOI: 10.18129/B9.bioc.genotypeeval    

QA/QC of a gVCF or VCF file

Bioconductor version: Release (3.6)

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 and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("genotypeeval")

Documentation

HTML		genotypeeval_vignette.html
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	BatchEffect, DataImport, Genetics, SNP, Sequencing, Software, VariantAnnotation
Version	1.10.0
In Bioconductor since	BioC 3.2 (R-3.2) (2.5 years)
License	file LICENSE
Depends	R (>= 3.3.0), VariantAnnotation
Imports	ggplot2, rtracklayer, BiocGenerics, GenomicRanges, GenomeInfoDb, IRanges, methods, BiocParallel, Rtsne, 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
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	genotypeeval_1.10.0.tar.gz
Windows Binary	genotypeeval_1.10.0.zip
Mac OS X 10.11 (El Capitan)	genotypeeval_1.10.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/genotypeeval
Package Short Url	http://bioconductor.org/packages/genotypeeval/
Package Downloads Report	Download Stats