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SHAPEIT5 is a software package to estimate haplotypes in large genotype datasets (WGS and SNP array).


Version 5.1.0 is now available! See the CHANGELOG for details.


If you use SHAPEIT5 in your research work, please cite the following paper:

Hofmeister RJ, Ribeiro DM, Rubinacci S., Delaneau O. Accurate rare variant phasing of whole-genome and whole-exome sequencing data in the UK Biobank.
Nature Genetics (2023) doi:

Get started now View source code on GitHub


SHAPEIT5 is composed of the following tools:

  • phase_common. Tool to phase common sites, typically SNP array data, or the first step of WES/WGS data phasing pipeline. This tool replaces SHAPEIT4.
  • ligate. Ligate multiple phased BCF/VCF files into a single whole chromosome file. Typically run to ligate multiple chunks of phased common variants.
  • phase_rare. Tool to phase rare variants onto a scaffold of common variants (output of phase_common / ligate).
  • switch. Program to compute switch error rate and genotyping error rate given simulated or trio data.
  • xcftools. Program to convert between the various file formats used by shapeit5 [BCF from/to XCF].

phase_common ligate phase_rare switch xcftools

Getting started

About the project

SHAPEIT5 is developed by Olivier Delaneau’s group.


SHAPEIT5 is distributed with MIT license.




SHAPEIT5 is an open source project and we very much welcome new contributors. When contributing to our repository, please first discuss the change you wish to make via issue, email, or any other method with the owners of this repository before making a change.

Thank you to the contributors of SHAPEIT5!

  • odelaneau
  • srubinacci
  • rwk-unil
  • diogomribeiro

We thank the Just the Docs developers, who made this awesome theme for Jekyll.

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Copyright © 2022-2023 Olivier Delaneau | All Rights Reserved | SHAPEIT5 executables and source code are distributed under the MIT license.