CGIL Centre for Genetic Improvement of Livestock

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                         Version 2.2

Genotype imputation


FImpute (ef-impute) was mainly developed for large scale genotype imputation in livestock where hundreds of thousands of individuals are genotypes with different panels. FImpute uses an overlapping sliding window approach to efficiently exploit relationships or haplotype similarities between target and reference individuals. The process starts with long windows to capture haplotype similarity between close relatives. After each chromosome sweep the window size is shrunk by a constant factor allowing for shorter haplotype similarity (arising from more distant relatives) to be taken into account. Because closer relatives usually share longer haplotypes while more distant relatives share shorter haplotypes the algorithm simply assumes that all individuals are related to each other at different degrees. Note that if pedigree information is provided FImpute makes use of this information for more accurate imputation. Pedigree information becomes more important as the low density panel becomes sparser. High input genotype quality is the key for accurate imputation with FImpute. The current version of FImpute can handle SNP markers only.

Download   (Last update: Jan, 2014)

  • Linux version

  • FImpute documentation (PDF)

  • Citing FImpute

    Sargolzaei, M., J. P. Chesnais and F. S. Schenkel. 2014. A new approach for efficient genotype imputation using information from relatives. BMC Genomics, 15:478 (DOI: 10.1186/1471-2164-15-478).


    The FImpute software is distributed "AS IS" solely for non-commercial use. The authors and their organizations will not be liable for any general, special, incidental or consequential damages arising from using FImpute. By the use of this software the user agrees to bear all risk resulting from using the software.