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Minimac3 is a tool for genotype imputation, an improved version of Minimac2. The Minimac Algorithm is a computationally efficient implementation of MaCH algorithm, works on phased genotypes and can handle large reference panels up to hundreds of thousands of haplotypes. It first identifies repeated haplotype patterns and uses these to speed up the computational process. Minimac3 uses less memory than its predecessors.


Population genetics


  • Operation: Imputation
  • Input: M3VCF (customized minimac3 VCF files)
  • Output: Standard VCF files
  • Software interface: Command-line user interface
  • Language: C++;C
  • Operating system: Linux
  • License: Other
  • Cost: Free
  • Version name: 2.0.1
  • Maturity: Stable
  • Credit: National Institutes of Health (NIH), Austrian Science Fund (FWF), the European Community's Seventh Framework Programme, the Intramural Research Program of the National Institute on Aging, National Institutes of Health
  • Contact: sayantan _at_
  • Collection: Minimac


Das S, Forer L, Schonherr S, Sidore C, Locke AE, Kwong A, Vrieze SI, Chew EY, Levy S, McGue M, Schlessinger D, Stambolian D, Loh PR, Iacono WG, Swaroop A, Scott LJ, Cucca F, Kronenberg F, Boehnke M, Abecasis GR, Fuchsberger C "Next-generation genotype imputation service and methods." Nat Genet. 2016 Oct;48(10):1284-1287.
PMID: 27571263
PMCID: PMC5157836

Fuchsberger C, Abecasis GR, Hinds DA "minimac2: faster genotype imputation." Bioinformatics. 2015 Mar 1;31(5):782-4. 2014 Oct 22.
PMID: 25338720
PMCID: PMC4341061

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