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: |
1.6 |
| 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: |
2022-02-15 |
| Author: |
Lindsay V. Clark 
[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 |
Documentation:
Downloads:
Reverse dependencies:
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