TY - JOUR T1 - Integrative haplotype estimation with sub-linear complexity JF - bioRxiv DO - 10.1101/493403 SP - 493403 AU - Olivier Delaneau AU - Jean-François Zagury AU - Matthew Robinson AU - Jonathan Marchini AU - Emmanouil Dermitzakis Y1 - 2018/01/01 UR - http://biorxiv.org/content/early/2018/12/13/493403.abstract N2 - 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. ER -