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LinkImputeR is a Java tool to call and impute genotypes. The LinkImputeR algorithm uses the read count information and all other available sequence information. LinkImputeR works particularly in non-model organisms because it does not need genotype reference panels or ordered markers.


Population genetics


  • Operation: Imputation
  • Input: VCF
  • Output: -
  • Software interface: Command-line user interface; Library
  • Language: Java;R
  • Operating system: Microsoft Windows, Mac OS X, Linux
  • License: Not stated
  • Cost: Free
  • Version name: 1.1.4
  • Maturity: Stable
  • Credit: Genome Canada Bioinformatics and Computational Biology, the Canada Research Chairs program, the National Sciences and Engineering Research Council of Canada.
  • Contact: Daniel Money _at_ | ZoĆ« Migicovsky zoe.migicovsky _at_ | Sean Myles sean.myles _at_
  • Collection: -


Money D, Migicovsky Z, Gardner K, Myles S "LinkImputeR: user-guided genotype calling and imputation for non-model organisms." BMC Genomics. 2017 Jul 10;18(1):523.
PMID: 28693460
PMCID: PMC5504746

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