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>.

Package details

AuthorLindsay V. Clark [aut, cre] (<https://orcid.org/0000-0002-3881-9252>), U.S. National Science Foundation [fnd]
MaintainerLindsay V. Clark <lvclark@illinois.edu>
LicenseGPL (>= 2)
Version1.2
URL https://github.com/lvclark/polyRAD
Package repositoryView on CRAN
Installation Install the latest version of this package by entering the following in R:
install.packages("polyRAD")

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polyRAD documentation built on July 2, 2020, 2:11 a.m.