SDFA: a standardized decomposition format and toolkit for efficient analysis of structural variants in large-scale population genomic studies

作者：Wenjie Peng, Liubin Zhang, Bin Tang, Junhao Liang, Zhi Liu, Lihang Ye, Yangyang Yuan, Yifei Wang, Rui Tan, Nan Lin, Chao Xue, Hui Jiang, Fang Li, Miaoxin Li · 发表于：Genome biology · 年份：2025 · DOI：10.1186/s13059-025-03730-3 · 研究领域：Genomics and Rare Diseases、Genetic Associations and Epidemiology、Epigenetics and DNA Methylation

Structural variants (SVs) contribute significantly to genetic diversity yet present computational challenges during analysis. We introduce SDFA, a standardized decomposition format and toolkit for efficient analysis of SVs in large-scale population genomics. SDFA efficiently stores and retrieves all SV types while providing algorithms for consistent SV merging, memory-efficient annotation, and precise gene feature annotation across large cohorts. SDFA outperforms existing tools, achieving at least 17.64 times faster merging than four tools and 120.93 times faster annotation than three tools, and uniquely handles complex SVs. We validate SDFA on 895,054 SVs from 150,119 individuals in the UK Biobank dataset.