| Title: | Statistical phasing of 150,119 sequenced genomes in the UK Biobank |
| Journal: | American Journal of Human Genetics |
| Published: | 29 Nov 2022 |
| Pubmed: | https://pubmed.ncbi.nlm.nih.gov/36450278/ |
| DOI: | https://doi.org/10.1016/j.ajhg.2022.11.008 |
| URL: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9892698 |
Publication 10726
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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.</p>
2 Authors
- Brian L Browning
- Sharon R Browning
1 Application
| Application ID | Title |
|---|---|
| 19934 | Statistical and Computational Genetics Methods Development |
Enabling scientific discoveries that improve human health