SHAPEIT specifications


Unique identifier OMICS_12566
Alternative name Segmented HAPlotype Estimation and Imputation Tool
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux, Mac OS
Computer skills Advanced
Version 2.0
Stability Stable
Maintained Yes



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  • person_outline Jean-François Zagury <>

SHAPEIT article

SHAPEIT citations

PMCID: 5719367

[…] allele frequency of at least 5%. a total of 447,617 markers (out of 786,799) were retained for analysis. genotypes were phased with the segmented haplotype estimation & imputation tool v2.r837 (shapeit2)33. the following parameter values were used: effective population size (neld) of 113, burn in of ten iterations, prune of ten iterations, 50 main iterations, 200 states, and windows of 500 […]

PMCID: 4731691

[…] mean on the first 2 principal components of the first 8 iterations of smartpca. the remaining 269,691 autosomal snps and 2,603 individuals were then imputed to 1000 genomes phase 1 (march 2012)11: shapeit v2 was used to phase the haplotypes and impute v2.2.2 was used to perform the imputation,12,13 resulting in 9,289,526 snps., we first tested genome-wide association with each autosomal snp, […]

SHAPEIT institution(s)
Chaire de Bioinformatique, Laboratoire Génomique, Bioinformatique, et Applications (Equipe d’accueil 4627), Conservatoire National des Arts et Métiers, Paris, France; Department of Statistics, University of Oxford, Oxford, UK

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