ArticleAmerican journal of human genetics2023
Statistical phasing of 150,119 sequenced genomes in the UK Biobank.
Article in American journal of human genetics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 28 citations in OpenAlex.
- ALGI: Sparse Convolutional Denoising Autoencoder Utilizing Local Genomic Information for Genotype Imputation.Animals : an open access journal from MDPI · 2026Article
- A novel method for across-chromosome phasing without relative data.Bioinformatics (Oxford, England) · 2026Article
- Advances in haplotype phasing and genotype imputation.Nature reviews. Genetics · 2026Review
- Real-world evaluation of gnomAD variant co-occurrence information for haplotype phasing in autosomal recessive disorders.Human genomics · 2025Article
- Modeling the length distribution of gene conversion tracts in humans from the UK Biobank sequence data.PLoS genetics · 2025Article
- Estimating gene conversion rates from population data using multi-individual identity by descent.American journal of human genetics · 2025Article
- Genome-wide association testing beyond SNPs.Nature reviews. Genetics · 2025Review
- Analysis-ready VCF at Biobank scale using Zarr.bioRxiv : the preprint server for biology · 2025Article
- Enabling efficient analysis of biobank-scale data with genotype representation graphs.Nature computational science · 2025Article
- Analysis-ready VCF at Biobank scale using Zarr.GigaScience · 2025Article
- A Genomics England haplotype reference panel and imputation of UK Biobank.Nature genetics · 2024Article
- Genotype Representation Graphs: Enabling Efficient Analysis of Biobank-Scale Data.bioRxiv : the preprint server for biology · 2024Article
- Improving population scale statistical phasing with whole-genome sequencing data.PLoS genetics · 2024Article
- Simultaneous estimation of genotype error and uncalled deletion rates in whole genome sequence data.PLoS genetics · 2024Article
- Biobank-scale inference of multi-individual identity by descent and gene conversion.American journal of human genetics · 2024Article
- Whole genome sequencing of 4,787 individuals identifies gene-based rare variants in age-related macular degeneration.Human molecular genetics · 2024Article
- Biobank-scale inference of multi-individual identity by descent and gene conversion.bioRxiv : the preprint server for biology · 2023Article
- Identity-by-descent-based estimation of the X chromosome effective population size with application to sex-specific demographic history.G3 (Bethesda, Md.) · 2023Article
- Accurate rare variant phasing of whole-genome and whole-exome sequencing data in the UK Biobank.Nature genetics · 2023Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
The first release of UK Biobank whole-genome sequence data contains 150,119 genomes. We present an open-source pipeline for filtering, phasing, and indexing these genomes on the cloud-based UK Biobank Research Analysis Platform. This pipeline makes it possible to apply haplotype-based methods to UK Biobank whole-genome sequence data. The pipeline uses BCFtools for marker filtering, Beagle for genotype phasing, and Tabix for VCF indexing. We used the pipeline to phase 406 million single-nucleotide variants on chromosomes 1-22 and X at a cost of £2,309. The maximum time required to process a chromosome was 2.6 days. In order to assess phase accuracy, we modified the pipeline to exclude trio parents. We observed a switch error rate of 0.0016 on chromosome 20 in the White British trio offspring. If we exclude markers with nonmajor allele frequency < 0.1% after phasing, this switch error rate decreases by 80% to 0.00032.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.