updog

Flexible Genotyping for Polyploids

Last update: 29 November 2023

Copyright license: GNU General Public License, version 3.0

Software version identifier: 2.1.3, 1.0.0, 1.0.1, 1.1.0, 1.1.1, 1.1.3, 1.2.0, 2.0.2, 2.1.1, 2.1.2, 2.1.4, 2.1.5

Description

Implements empirical Bayes approaches to genotype polyploids from next generation sequencing data while accounting for allele bias, overdispersion, and sequencing error. The main functions are flexdog() and multidog(), which allow the specification of many different genotype distributions. Also provided are functions to simulate genotypes, rgeno(), and read-counts, rflexdog(), as well as functions to calculate oracle genotyping error rates, oracle_mis(), and correlation with the true genotypes, oracle_cor(). These latter two functions are useful for read depth calculations. Run browseVignettes(package = "updog") in R for example usage. See Gerard et al. (2018) <doi:10.1534/genetics.118.301468> and Gerard and Ferrao (2020) <doi:10.1093/bioinformatics/btz852> for details on the implemented methods.

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