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FINDHAP

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.
FieldValue
Modified
2019-08-05
Release Date
2019-04-29
Identifier
32c52e5f-073f-4386-bb97-f9cca46a6fbf
Publisher
United States Department of Agriculture
License
Contact Name
Hubbard, Suzanne
Contact Email
Public Access Level
Public
Program Code
005:040 - Department of Agriculture - National Research
Bureau Code
005:18 - Agricultural Research Service