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A tool for rare variant genotype imputation. The GIGI algorithm can handle large pedigrees. Only a subset of individuals in a pedigree needs to be completely sequenced, GIGI will infer the missing genotypes at untyped markers, if the remaining individuals are sequenced solely at appropriate marker locations. GIGI-Quick can speed up the computation by running GIGI in parallel. See 'links'.


Population genetics


  • Operation: Imputation
  • Software interface: Command-line user inteface
  • Language: C++
  • Operating system: Microsoft Windows, Mac OS X, Linux
  • License: Not stated
  • Cost: Free
  • Version name: 1.06.1
  • Maturity: Stable
  • Credit: The National Institutes of Health (NIH)
  • Contact: Ellen M. Wijsman wijsman _at_
  • Collection: GIGI


Cheung CY, Thompson EA, Wijsman EM "GIGI: an approach to effective imputation of dense genotypes on large pedigrees." Am J Hum Genet. 2013 Apr 4;92(4):504-16.
PMID: 23561844
PMCID: PMC3617386

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