SHAPEIT pipeline

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 <>

Publication for Segmented HAPlotype Estimation and Imputation Tool

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: 4754680

[…] little recombination occurs within loci, we examined the decay in linkage disequilibrium (ld) with distance between pairs of snps in our data using snp data in vcf files, which were phased using shapeit2 (v 2.790)40, and analysed using vcftools (v0.1.11) –hap-r2 and found that ld decays to background levels for distances great than around 400kb (supplementary fig. s5). to be conservative, […]

PMCID: 4700947

[…] et al. 2013) that generally rely on a pre-existent reference list of preassembled haplotypes to accurately generate phase information. we therefore phased the genotypes from the previous step using shapeit (v2) software (delaneau et al. 2013) and the 1000 genomes project data as the reference panel of haplotypes. following the software recommendations, all genotypes were simultaneously phased […]

PMCID: 3585000

[…] using plink on pruned snps. the mds was performed in the r environment [30]., pca was performed using smartpca, part of the eigensoft 3.0 package [17]., samples (505,859 snps) were phased with shapeit [31] using as a reference the hapmap3 genetic maps [32]. a coancestry matrix was constructed using chromopainter [16] with the default settings. finestructure [16] was used to perform an mcmc […]

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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