GBS data normally have high error rate for heterozygote sites. ImputeR is a package to infer the most likely genotypes using raw GBS data.

Install devtools first, and then use devtools to install imputeR from github.

devtools::install_github("hadley/devtools")
library(devtools)
install_github("yangjl/imputeR")
library(imputeR)

A vignette can be found here. Documented functions are listed as below. Their usage information can be found by typing ?function_name or help(function_name).

• impute_parent

• getsfs: setup the neutral SFS
• error_mx and gen_error_mat: get genotype error matrix for mom and kids.