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.
- Version2.0.0
- R version≥ 3.5.0 methods
- LicenseGPL-2
- LicenseGPL-3
- Needs compilation?Yes
- polyRAD citation info
- Last release11/06/2022
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Team
Lindsay V. Clark
U.S. National Science Foundation
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- Imports3 packages
- Suggests5 packages
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