Imputation of low-coverage sequencing data from 150,119 UK Biobank genomes
Simone Rubinacci, Robin J. Hofmeister, Bárbara Sousa da Mota, Olivier Delaneau
Abstract
The release of 150,119 UK Biobank sequences represents an unprecedented opportunity as a reference panel to impute low-coverage whole-genome sequencing data with high accuracy but current methods cannot cope with the size of the data. Here we introduce GLIMPSE2, a low-coverage whole-genome sequencing imputation method that scales sublinearly in both the number of samples and markers, achieving efficient whole-genome imputation from the UK Biobank reference panel while retaining high accuracy for ancient and modern genomes, particularly at rare variants and for very low-coverage samples.
Topics & Concepts
BiobankImputation (statistics)BiologyGenome1000 Genomes ProjectComputational biologyWhole genome sequencingDNA sequencingMissing dataGeneticsData miningStatisticsComputer scienceDNASingle-nucleotide polymorphismGeneGenotypeMathematicsGenetic Associations and EpidemiologyGenetic factors in colorectal cancerCancer-related molecular mechanisms research