updog - Flexible Genotyping for Polyploids
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.