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, or genotypes sampled from those probabilties, can then be exported for downstream analysis. 'polyRAD' is described by Clark et al. (2018) .


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1.0 by Lindsay V. Clark, 3 months ago

Browse source code at

Authors: Lindsay V. Clark [aut, cre] , U.S. National Science Foundation [fnd]

Documentation:   PDF Manual  

GPL (>= 2) license

Imports fastmatch, pcaMethods, methods, Rcpp

Suggests rrBLUP, Rsamtools, GenomeInfoDb, Biostrings, GenomicRanges, VariantAnnotation, SummarizedExperiment, S4Vectors, IRanges, BiocGenerics, knitr, rmarkdown, GenomicFeatures, qqman

Linking to Rcpp

See at CRAN