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SHAPEIT (Segmented HAPlotype Estimation and Imputation Tool) is a tool to estimate haplotypes. The SHAPEIT algorithm uses data from unrelated individuals or small families and scales linearly with he number of single-nucleotide polymorphisms (SNPs) and haplotypes.


Genotype and phenotype; Genotyping experiment


  • Operation: Imputation; Haplotype mapping
  • Output: HAPS/SAMPLE format
  • Software interface: Command-line user interface
  • Language: C++
  • Operating system: Linux
  • License: Other
  • Cost: Free for non-commercial use
  • Version name: 2.12
  • Maturity: Stable
  • Credit: Agence Nationale de Recherches sur le SIDA et les Hépatites, Centre de Recherches et d’investigations épidermiques et sensorielles, Medical Research Council,
  • Contact: Prof. Zagury zagury _at_ | Prof. Marchini marchini _at_
  • Collection: -


Delaneau O, Marchini J, Zagury JF "A linear complexity phasing method for thousands of genomes." Nat Methods. 2011 Dec 4;9(2):179-81.
PMID: 22138821

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