polyRAD

MaRDI QIDQ90619CRANFDO

Authors Lindsay V Clark

Last update 22 March 2026

Copyright license GNU General Public License, version 2.0, GNU General Public License, version 3.0

Software version identifier 2.0.0, PACKAGES.rds, 0.5-0, 1.0, 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 2.0.1

Description

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>.

Cites work

• A population-level statistic for assessing Mendelian behavior of genotyping-by-sequencing data from highly duplicated genomes
• A population-level statistic for assessing Mendelian behavior of genotyping-by-sequencing data from highly duplicated genomes
• polyRAD: Genotype Calling with Uncertainty from Sequencing Data in Polyploids and Diploids

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