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- W4310572148 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." @default.
- W4310572148 created "2022-12-12" @default.
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- W4310572148 date "2023-01-01" @default.
- W4310572148 modified "2023-10-04" @default.
- W4310572148 title "Statistical phasing of 150,119 sequenced genomes in the UK Biobank" @default.
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- W4310572148 doi "https://doi.org/10.1016/j.ajhg.2022.11.008" @default.
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