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>, and the Hind/He statistic for marker filtering is described by Clark et al. (2022) <doi:10.1186/s12859-022-04635-9>. A variant calling pipeline for highly duplicated genomes is also included and is described by Clark et al. (2020, Version 1) <doi:10.1101/2020.01.11.902890>.

Version: 2.0.0
Depends: R (≥ 3.5.0), methods
Imports: fastmatch, pcaMethods, Rcpp, stringi
LinkingTo: Rcpp
Suggests: rrBLUP, Rsamtools, GenomeInfoDb, Biostrings, GenomicRanges, VariantAnnotation, SummarizedExperiment, S4Vectors, IRanges, BiocGenerics, knitr, rmarkdown, GenomicFeatures, ggplot2, adegenet
Published: 2022-11-06
DOI: 10.32614/CRAN.package.polyRAD
Author: Lindsay V. Clark ORCID iD [aut, cre], U.S. National Science Foundation [fnd]
Maintainer: Lindsay V. Clark <Lindsay.Clark at seattlechildrens.org>
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


Reference manual: polyRAD.pdf
Vignettes: Variant and Genotype Calling in Highly Duplicated Genomes
polyRAD Tutorial


Package source: polyRAD_2.0.0.tar.gz
Windows binaries: r-devel: polyRAD_2.0.0.zip, r-release: polyRAD_2.0.0.zip, r-oldrel: polyRAD_2.0.0.zip
macOS binaries: r-release (arm64): polyRAD_2.0.0.tgz, r-oldrel (arm64): polyRAD_2.0.0.tgz, r-release (x86_64): polyRAD_2.0.0.tgz, r-oldrel (x86_64): polyRAD_2.0.0.tgz
Old sources: polyRAD archive

Reverse dependencies:

Reverse suggests: polymapR


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