Accurate, scalable and integrative haplotype estimation.

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State: Public
Version: Final published version
License: CC BY 4.0
Serval ID
serval:BIB_B07D06940616
Type
Article: article from journal or magazin.
Collection
Publications
Institution
Title
Accurate, scalable and integrative haplotype estimation.
Journal
Nature communications
Author(s)
Delaneau O., Zagury J.F., Robinson M.R., Marchini J.L., Dermitzakis E.T.
ISSN
2041-1723 (Electronic)
ISSN-L
2041-1723
Publication state
Published
Issued date
28/11/2019
Peer-reviewed
Oui
Volume
10
Number
1
Pages
5436
Language
english
Notes
Publication types: Journal Article ; Research Support, Non-U.S. Gov't
Publication Status: epublish
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.
Keywords
Biological Specimen Banks, Data Interpretation, Statistical, Datasets as Topic, Genotype, Haplotypes, High-Throughput Nucleotide Sequencing, Humans, Polymorphism, Single Nucleotide, Sample Size, Sequence Analysis, DNA, Software
Pubmed
Web of science
Open Access
Yes
Create date
11/12/2019 8:01
Last modification date
30/04/2021 6:13
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