Haplotype estimation for biobank-scale data sets.
The UK Biobank (UKB) has recently released genotypes on 152,328 individuals together with extensive phenotypic and lifestyle information. We present a new phasing method, SHAPEIT3, that can handle such biobank-scale data sets and results in switch error rates as low as ∼0.3%. The method exhibits O(NlogN) scaling with sample size N, enabling fast and accurate phasing of even larger cohorts.
Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.|Department of Statistics, University of Oxford, Oxford, UK.
Jared
J
O'Connell
Department of Statistics, University of Oxford, Oxford, UK.
Kevin
K
Sharp
Department of Health Sciences, University of Leicester, Leicester, UK.
Nick
N
Shrine
Department of Health Sciences, University of Leicester, Leicester, UK.
Louise
L
Wain
School of Medicine, University of Nottingham, Nottingham, UK.
Ian
I
Hall
Department of Health Sciences, University of Leicester, Leicester, UK.
Martin
0000-0002-3596-7874
M
Tobin
Chaire de Bioinformatique, Laboratoire Génomique, Bioinformatique et Applications (Equipe d'Accueil 4627), Conservatoire National des Arts et Métiers, Paris, France.
Jean-Francois
JF
Zagury
Département de Génétique et Développement, University of Geneva, Geneva, Switzerland.
Olivier
O
Delaneau
Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.|Department of Statistics, University of Oxford, Oxford, UK.
Jonathan
0000-0003-0610-8322
J
Marchini
D000465:Algorithms; D018070:Biological Specimen Banks; D015331:Cohort Studies; D019295:Computational Biology / Q000379:methods*; D066264:Datasets as Topic; D005828:Genetics, Population; D015894:Genome, Human; D023281:Genomics; D006239:Haplotypes / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing / Q000706:statistics & numerical data; D006801:Humans; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D017422:Sequence Analysis, DNA / Q000379:methods; D006113:United Kingdom; D044465:White People