The findhap.f90 program finds haplotypes and imputes genotypes using multiple chip sets and sequence data. Program and download information can be found at the Animal Improvement Program (AIP) web site: http://aipl.arsusda.gov/software/findhap

Downloads
Version 4 program, example files, and executable
(beta version — not quite ready for routine use on U.S. chip data, but performs better than version 3 for sequence data)

Example data files for imputation study presented by VanRaden and Sun at the 2014 World Congress on Genetics Applied to Livestock Production

• Files include actual pedigree, simulated true genotypes, simulated sequence reads, and imputed genotypes.
• This example used 500 reference bulls sequenced at 4× with 1% error and containing high-density SNPs; the 250 young bulls used to test imputation had only high-density SNPs.
• Other examples in the study can be generated by setting other options for programs findhap4, geno2seq, and genosim.