ArticleAmerican journal of human genetics2021
Fast two-stage phasing of large-scale sequence data.
Article in American journal of human genetics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 519 papers, 2 of them syntheses that pooled it.
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Who cites it
519 citing papers in PubMed, 2 syntheses or guidelines pooled it.
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- The genetic basis of dermatophytosis skin infection susceptibility.Nature communications · 2026Pooled it
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- Pre-divergence hybridization and adaptive introgression shaped the genetic architecture of East Asian domestic pigs.Science China. Life sciences · 2026Article
- Message in a bottleneck: Nested founder effects from French Polynesia to Rapa Nui and Hawai'i.Science (New York, N.Y.) · 2026Article
- Pan-cancer prevalence of microsatellite instability and Lynch syndrome in India.Familial cancer · 2026Article
- Host genetic variation is associated with root-associated microbiome assembly and resistance to Fusarium oxysporum in tobacco.Plant physiology · 2026Article
- Drift and Selection in a Recently Colonized Sea: The Genomic Basis of Adaptation to Low-Salinity Waters in Baltic Harbour Porpoises.Molecular ecology · 2026Article
- A Large-Scale Cross-Population Evaluation of Genetic Risk Variants for Dilated Cardiomyopathy in Dobermanns.Animal genetics · 2026Article
- Novel genetic profile linked to cognitive decline in Hispanics/Latinos.Alzheimer's & dementia : the journal of the Alzheimer's Association · 2026Article
- A Selective Sweep Likely Linked to Xenobiotic Detoxification Identified Along Altitudinal Gradients in the Pine Processionary Moth.Genome biology and evolution · 2026Article
- Explaining the unexplained admixture mapping signals via rare variants: the HCHS/SOL.Human molecular genetics · 2026Article
- Historical introgression from commercial meat-type ducks constitutes the common genetic basis of white plumage in egg-type duck breeds.Poultry science · 2026Article
- Twenty-one years of three-way hybrid breeding shaped diversity and complementarity of male and female gene pools in sugar beet.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
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- Discovering common and population-specific QTLs for leaf rust resistance in different Barley populations.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- Genetic architecture and evolution of stripe rust resistance uncovered using diverse panels of wheat lines and North American Puccinia striiformis f. sp. tritici isolates.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- Genetic Diversity and Selection Signatures of Two North American Corriente Cattle Herds in Northeastern New Mexico, United States.International journal of molecular sciences · 2026Article
- Whole-Genome Sequencing Reveals Population Structure, Genetic Diversity, and Selection Signatures in Kazakh Dromedary and Bactrian Camels.Animals : an open access journal from MDPI · 2026Article
- Genome-Wide Differentiation, Inbreeding, and Candidate Selection Loci in Local Vietnamese Pig Breeds.International journal of molecular sciences · 2026Article
459 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors.
Funding
Abstract
Haplotype phasing is the estimation of haplotypes from genotype data. We present a fast, accurate, and memory-efficient haplotype phasing method that scales to large-scale SNP array and sequence data. The method uses marker windowing and composite reference haplotypes to reduce memory usage and computation time. It incorporates a progressive phasing algorithm that identifies confidently phased heterozygotes in each iteration and fixes the phase of these heterozygotes in subsequent iterations. For data with many low-frequency variants, such as whole-genome sequence data, the method employs a two-stage phasing algorithm that phases high-frequency markers via progressive phasing in the first stage and phases low-frequency markers via genotype imputation in the second stage. This haplotype phasing method is implemented in the open-source Beagle 5.2 software package. We compare Beagle 5.2 and SHAPEIT 4.2.1 by using expanding subsets of 485,301 UK Biobank samples and 38,387 TOPMed samples. Both methods have very similar accuracy and computation time for UK Biobank SNP array data. However, for TOPMed sequence data, Beagle is more than 20 times faster than SHAPEIT, achieves similar accuracy, and scales to larger sample sizes.
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