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. Resources in this dataset:Resource Title: FINDHAP. File Name: Web Page, url: https://www.ars.usda.gov/research/software/download/?softwareid=494&modecode=80-42-05-30 download page