polyRAD: Genotype Calling with Uncertainty from Sequencing Data in Polyploids and Diploids

Read depth data from genotyping-by-sequencing (GBS) or restriction site-associated DNA sequencing (RAD-seq) are imported and used to make Bayesian probability estimates of genotypes in polyploids or diploids. The genotype probabilities, posterior mean genotypes, or most probable genotypes can then be exported for downstream analysis. 'polyRAD' is described by Clark et al. (2019) <doi:10.1534/g3.118.200913>. A variant calling pipeline for highly duplicated genomes is also included and is described by Clark et al. (2020) <doi:10.1101/2020.01.11.902890>.

Version: 1.3
Depends: R (≥ 3.5.0)
Imports: fastmatch, pcaMethods, methods, Rcpp
LinkingTo: Rcpp
Suggests: rrBLUP, Rsamtools, GenomeInfoDb, Biostrings, GenomicRanges, VariantAnnotation, SummarizedExperiment, S4Vectors, IRanges, BiocGenerics, knitr, rmarkdown, GenomicFeatures, qqman, ggplot2
Published: 2021-01-06
Author: Lindsay V. Clark ORCID iD [aut, cre], U.S. National Science Foundation [fnd]
Maintainer: Lindsay V. Clark <lvclark at illinois.edu>
License: GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
URL: https://github.com/lvclark/polyRAD
NeedsCompilation: yes
Citation: polyRAD citation info
Materials: NEWS
CRAN checks: polyRAD results

Downloads:

Reference manual: polyRAD.pdf
Vignettes: Variant and Genotype Calling in Highly Duplicated Genomes
polyRAD Tutorial
Package source: polyRAD_1.3.tar.gz
Windows binaries: r-devel: polyRAD_1.3.zip, r-release: polyRAD_1.3.zip, r-oldrel: polyRAD_1.3.zip
macOS binaries: r-release: polyRAD_1.3.tgz, r-oldrel: polyRAD_1.3.tgz
Old sources: polyRAD archive

Reverse dependencies:

Reverse suggests: polymapR

Linking:

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