2022
DOI: 10.1101/2022.11.28.518213
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Imputation of low-coverage sequencing data from 150,119 UK Biobank genomes

Abstract: Recent work highlights the advantages of low-coverage whole genome sequencing (lcWGS), followed by genotype imputation, as a cost-effective genotyping technology for statistical and population genetics. The release of whole genome sequencing data for 150,119 UK Biobank (UKB) samples represents an unprecedented opportunity to impute lcWGS with high accuracy. However, despite recent progress, current methods struggle to cope with the growing numbers of samples and markers in modern reference panels, resulting in… Show more

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Cited by 19 publications
(22 citation statements)
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“…S2A). These ancient Jomon genomes were imputed and phased by GLIMPSE2 software ( 17 ), a tool designed for imputation of low-coverage genomic sequences. Given that approximately 20% of their genomic components of modern Hondo Japanese are reported to be derived from the Jomon people ( 6 , 13 , 14 ), and considering the absence of available direct descendants from the Jomon people in current populations today with the exception of Japanese archipelago populations, employing the modern Japanese as a reference was deemed necessary for the imputation of the Jomon genomes.…”
Section: Resultsmentioning
confidence: 99%
See 1 more Smart Citation
“…S2A). These ancient Jomon genomes were imputed and phased by GLIMPSE2 software ( 17 ), a tool designed for imputation of low-coverage genomic sequences. Given that approximately 20% of their genomic components of modern Hondo Japanese are reported to be derived from the Jomon people ( 6 , 13 , 14 ), and considering the absence of available direct descendants from the Jomon people in current populations today with the exception of Japanese archipelago populations, employing the modern Japanese as a reference was deemed necessary for the imputation of the Jomon genomes.…”
Section: Resultsmentioning
confidence: 99%
“…We then conducted genotype imputation and haplotype phasing for the Jomon genomes including low-coverage individuals using GLIMPSE2 ( 17 ). We used phased VCF files from 9,290 modern Japanese individuals, reported by Kawai et al, (2023) ( 18 ), as the reference panel, along with 2,482 individuals from the 1000 Genomes Project including 104 Japanese individuals ( 19 ).…”
Section: Methodsmentioning
confidence: 99%
“…To assess the performance of the phasing, we set Ne = 1000 with other parameters in default for both software. Then, we chose QUILT v1.0.4 [7] and GLIMPSE2 [25] as lcWGS imputation software and both accept bam files as an input. In addition, we also use Beagle v5.4 [26] to impute chip data based on a previous study [27] on cattle.…”
Section: Methodsmentioning
confidence: 99%
“…f) Imputation performance evaluation In order to evaluate the imputation accuracy in both experiments, we used GLIMPSE_concordance from GLIMPSE v2 56 ). The evaluation process was restricted to sites that had a minimum of eight reads and a genotype posterior probability of at least 0.9999.…”
Section: D) Genotype Callingmentioning
confidence: 99%