Open-source benchmarking of IBD segment detection methods for biobank-scale cohorts

Area of Science:

• Genetics
• Bioinformatics
• Population Genetics

Background:

• The biobank era has increased interest in identical-by-descent (IBD) segment detection for population and genealogical studies.
• Existing benchmarks for IBD detection methods lack standardization, using different datasets, suboptimal parameters, and inconsistent metrics.
• A fair and comprehensive comparison of IBD detection tools is needed.

Purpose of the Study:

• To develop a comprehensive and open-source evaluation framework for IBD segment detection methods.
• To assess the power, accuracy, and resource consumption of various IBD detection tools.
• To provide a practical guide for users selecting IBD detection methods.

Main Methods:

• Developed a completely open-source evaluation system.
• Utilized realistic population genetic simulations with diverse settings.
• Assessed methods based on power, accuracy, and computational resource consumption.

Main Results:

• Established a standardized benchmark for evaluating IBD detection methods.
• Provided a detailed comparison of different IBD detection tools.
• Identified optimal parameters and performance metrics for IBD detection.

Conclusions:

• The developed framework enables fair and reproducible evaluation of IBD detection methods.
• Results offer practical guidance for researchers in selecting appropriate IBD detection tools.
• This work facilitates advancements in population genetics and haplotype association studies.