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A pipeline tool for genotype imputation. The genipe algorithm includes imputed data indexing, data management, Sequence Kernel Association Test, Cox proportional hazards for survival analysis, linear mixed models for repeated measurements in longitudinal studies. The imputation pipeline works with PLINK, SHAPEIT, and IMPUTE2.


Population genetics


  • Operation: Imputation
  • Software interface: Command-line user interface
  • Language: Python
  • Operating system: Linux
  • License: open source
  • Cost: Free
  • Version name: 1.4.2
  • Maturity: Stable
  • Credit: Montreal Heart Institute Foundation, Genome Canada, Genome Quebec.
  • Contact: louis-philippe.lemieux.perreault _at_ | marie-pierre.dube _at_
  • Collection: -


Lemieux Perreault LP, Legault MA, Asselin G, Dube MP "genipe: an automated genome-wide imputation pipeline with automatic reporting and statistical tools." Bioinformatics. 2016 Dec 1;32(23):3661-3663. Epub 2016 Aug 6.
PMID: 27497439
PMCID: PMC5181529

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