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Accurate, scalable and integrative haplotype estimation.

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.

SUBMITTER: Delaneau O

PROVIDER: S-EPMC6882857 | biostudies-literature | 2019 Nov

REPOSITORIES: biostudies-literature

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Accurate, scalable and integrative haplotype estimation.

Delaneau Olivier O Zagury Jean-François JF Robinson Matthew R MR Marchini Jonathan L JL Dermitzakis Emmanouil T ET

Nature communications 20191128 1

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 ...[more]

PMID: 31780650

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