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Nat Commun. 2019 Nov 28;10(1):5436. doi: 10.1038/s41467-019-13225-y.

Accurate, scalable and integrative haplotype estimation.

Author information

1
Department of Computational Biology, University of Lausanne, Génopode, 1015, Lausanne, Switzerland. olivier.delaneau@unil.ch.
2
Swiss Institute of Bioinformatics (SIB), University of Lausanne, Quartier Sorge - Batiment Amphipole, 1015, Lausanne, Switzerland. olivier.delaneau@unil.ch.
3
Chaire de Bioinformatique, Laboratoire GBCM (EA7528), Conservatoire National des Arts et Métiers, HESAM Université, Paris, France.
4
Department of Computational Biology, University of Lausanne, Génopode, 1015, Lausanne, Switzerland.
5
Swiss Institute of Bioinformatics (SIB), University of Lausanne, Quartier Sorge - Batiment Amphipole, 1015, Lausanne, Switzerland.
6
Department of Statistics, University of Oxford, 24-29 St. Giles, Oxford, OX1 3LB, UK.
7
Department of Genetic Medicine and Development, University of Geneva Medical School, 1 rue Michel-Servet, 1211, Geneva, Switzerland.
8
Swiss Institute of Bioinformatics (SIB), University of Geneva, 1 rue Michel-Servet, 1211, Geneva, Switzerland.
9
Institute of Genetics and Genomics in Geneva, University of Geneva Medical School, 1 rue Michel-Servet, 1211, Geneva, Switzerland.

Abstract

The number of human genomes being genotyped or sequenced increases exponentially and efficient haplotype estimation methods able to handle this amount of data are now required. Here we present a method, SHAPEIT4, which substantially improves upon other methods to process large genotype and high coverage sequencing datasets. It notably exhibits sub-linear running times with sample size, provides highly accurate haplotypes and allows integrating external phasing information such as large reference panels of haplotypes, collections of pre-phased variants and long sequencing reads. We provide SHAPEIT4 in an open source format and demonstrate its performance in terms of accuracy and running times on two gold standard datasets: the UK Biobank data and the Genome In A Bottle.

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