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 
[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 [issues need fixing before 2026-03-30] |
Documentation:
Downloads:
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