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chipimputation is a pipeline tool for genotype imputation. The chipimputation pipeline consists of Perl and Python scripts and incorporates the following software tools: PLINK, Shapeit, Impute2, and gtool.


Population genetics


  • Operation: Imputation
  • Software interface: Command-line user interface
  • Language: Perl, Python
  • Operating system: Linux
  • License: The MIT licence
  • Cost: Free
  • Version name: 1.0
  • Maturity: Stable
  • Credit: National Human Genome Research Institute (NHGRI), the Office Of The Director (OD), National Institutes of Health.
  • Contact: -
  • Collection: H3ABioNet


Baichoo S, Souilmi Y, Panji S, Botha G, Meintjes A, Hazelhurst S, Bendou H, Beste E, Mpangase PT, Souiai O, Alghali M, Yi L, O'Connor BD, Crusoe M, Armstrong D, Aron S, Joubert F, Ahmed AE, Mbiyavanga M, Heusden PV, Magosi LE, Zermeno J, Mainzer LS, Fadlelmola FM, Jongeneel CV, Mulder N "Developing reproducible bioinformatics analysis workflows for heterogeneous computing environments to support African genomics." BMC Bioinformatics. 2018 Nov 29;19(1):457.
PMID: 30486782
PMCID: PMC6264621

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