FINDHAP

<p>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: <a href="http://aipl.arsusda.gov/software/findhap">http://aipl.arsusda.gov/software/findhap</a></p> <p><strong>Downloads</strong> 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)</p> <p><a href="https://aipl.arsusda.gov/software/findhap/SequenceFiles.zip">Example data files</a> for <a href="https://asas.org/docs/default-source/wcgalp-proceedings-oral/179_paper_9110_manuscript_445_0.pdf">imputation study</a> presented by VanRaden and Sun at the 2014 World Congress on Genetics Applied to Livestock Production</p> <ul> <li>Files include actual pedigree, simulated true genotypes, simulated sequence reads, and imputed genotypes.</li> <li>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.</li> <li> <p>Other examples in the study can be generated by setting other options for programs findhap4, geno2seq, and genosim.</p> <div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: FINDHAP.</p> <p>File Name: Web Page, url: <a href="https://www.ars.usda.gov/research/software/download/?softwareid=494&modecode=80-42-05-30" target="_blank">https://www.ars.usda.gov/research/software/download/?softwareid=494&modecode=80-42-05-30</a> </p><p>download page</p></li></ul> </li> </ul>

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