ArticleGenetics, selection, evolution : GSE2024
Empirical versus estimated accuracy of imputation: optimising filtering thresholds for sequence imputation.
Article in Genetics, selection, evolution : GSE, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- Imputation in the Wild: Genome-Wide Robustness and Fine-Scale Limitations of Low-Coverage Genomes in Endangered Species.Molecular ecology resources · 2026Article
- Article
- Genomic platform specific polygenic risk scores impact breast cancer risk stratification.Communications medicine · 2025Article
- Integrating extensive functional annotations and multiomics of cattle enhances climate resilience prediction and mapping.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Comparison between SNP array and imputed data to estimate population structure and ROH hotspots in horse breeds.BMC genomics · 2025Article
- Genotype imputation from low-coverage data for medical and population genetic analyses.Genome research · 2025Article
- Machine learning solutions for integrating partially overlapping genetic datasets and modelling host-endophyte effects in ryegrass (Frontiers in plant science · 2025Article
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundGenotype imputation is a cost-effective method for obtaining sequence genotypes for downstream analyses such as genome-wide association studies (GWAS). However, low imputation accuracy can increase the risk of false positives, so it is important to pre-filter data or at least assess the potential limitations due to imputation accuracy. In this study, we benchmarked three different imputation programs (Beagle 5.2, Minimac4 and IMPUTE5) and compared the empirical accuracy of imputation with the software estimated accuracy of imputation (Rsq
resultsThe accuracy of imputing sequence variants from real high-density genotypes was higher than from low-density genotypes. In our software benchmark, all programs performed well with only minor differences in accuracy. While there was a close relationship between empirical imputation accuracy and the imputation Rsq
conclusionsThis study provides an empirically derived approach to apply customised software-specific Rsq
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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 Socratic graph.