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bioRxiv · 10.1101/493403

Integrative haplotype estimation with sub-linear complexity

Delaneau, O.·Zagury, J.-F.·Robinson, M. R.·Marchini, J.·Dermitzakis, E.
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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 new method, SHAPEIT4, which substantially improves upon other methods to process large genotype and high coverage sequencing datasets. It notably exhibits sub-linear scaling 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 SHAPET4 in an open source format on https://odelaneau.github.io/shapeit4/ 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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Delaneau, O., Zagury, J.-F., Robinson, M. R., Marchini, J., Dermitzakis, E.. 2018-12-13. Integrative haplotype estimation with sub-linear complexity. https://doi.org/10.1101/493403

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