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NPUTE is a tool for genotype imputation. The NPUTE algorithm uses the K-nearest-neighbor (KNN) over any size of sliding haplotype window method, a mismatch accumulator array (MAA). NPUTE also estimates the imputation accuracy by inference of known SNP values when left out.


Population genetics


  • Operation: Imputation
  • Software interface: Command-line user interface
  • Language: Python
  • Operating system: Mac OS X; Linux
  • License: Open source
  • Cost: Free
  • Version name: v1
  • Maturity: Stable
  • Credit: The United States Environmental Protection Agency (EPA), the National Institutes of Health (NIH), the National Science Foundation (NSF), Division of Information and Intelligent Systems (IIS).
  • Contact: ajr _at_ | Leonard McMillan mcmillan _at_
  • Collection: -


Roberts A, McMillan L, Wang W, Parker J, Rusyn I, Threadgill D "Inferring missing genotypes in large SNP panels using fast nearest-neighbor searches over sliding windows." Bioinformatics. 2007 Jul 1;23(13):i401-7.
PMID: 17646323

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