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EagleImp: fast and accurate genome-wide phasing and imputation in a single tool
Lars Wienbrandt1, David Ellinghaus1,2
1Institute of Clinical Molecular Biology, Kiel University, 24105 Kiel, Germany.
Bioinformatics (Oxford, England)
|September 21, 2022
Summary
EagleImp accelerates reference-based phasing and genotype imputation, offering significant speedups over existing tools while maintaining high accuracy. This new software is optimized for large-scale genomic datasets, including future panels of up to 1 million genomes.
Area of Science:
- Genomics
- Bioinformatics
- Computational Biology
Background:
- Reference-based phasing and genotype imputation are crucial for genetic analysis.
- Existing algorithms, despite theoretical sublinear runtimes, face practical challenges with large genome-wide reference datasets.
- High computational costs limit the scalability of current phasing and imputation methods.
Purpose of the Study:
- To develop a novel software tool, EagleImp, for accelerated and accurate reference-based phasing and genotype imputation.
- To improve upon existing methods by incorporating algorithmic and technical enhancements.
- To provide a scalable solution for handling large genomic reference panels.
Main Methods:
- Developed EagleImp based on established methods from Eagle2 and PBWT.
- Implemented algorithmic and technical improvements for enhanced performance.
- Evaluated EagleImp against Eagle2, PBWT, and imputation servers using diverse whole-genome sequencing datasets (1000 Genomes, HRC, simulated data).
Main Results:
- EagleImp demonstrated 2-30 times faster runtimes compared to Eagle2 combined with PBWT.
- Achieved equivalent or superior phasing and imputation quality across all tested scenarios.
- Outperformed leading imputation services (Sanger, Michigan, TOPMed) for common variants, even with larger reference panels.
- Incorporated features like automated chromosome splitting and memory management for robust handling of large files.
Conclusions:
- EagleImp offers a significant advancement in computational efficiency and accuracy for reference-based phasing and imputation.
- The software is optimized for current and future large-scale genomic reference panels.
- EagleImp provides a powerful and accessible tool for genetic research, facilitating large-scale genome-wide association studies.
