Benchmarking of germline copy number variant callers from whole genome sequencing data for clinical applications

Motivation: Whole-genome sequencing (WGS) is increasingly preferred for clinical applications due to its comprehensive coverage, effectiveness in detecting copy number variants (CNVs), and declining costs. However, systematic evaluations of WGS CNV callers tailored to germline clinical testing-where high sensitivity and confirmation of reported CNVs are essential-remain necessary. Clinical reporting typically emphasizes CNVs affecting coding regions over precise breakpoint detection. This study benchmarks several short-read WGS CNV detection tools using reference cell lines to inform their clinical use. Results: While tools vary in sensitivity (7%-83%) and precision (1%-76%), few meet the sensitivity needed for clinical testing. Callers generally perform better for deletions (up to 88% sensitivity) than duplications (up to 47% sensitivity), with poor detection of duplications under 5 kb. Notably, for CNVs in genes commonly included in clinical panels, significantly improved sensitivity and precision were observed when benchmarking against 25 cell lines with known CNVs. DRAGEN v4.2 high-sensitivity CNV calls, post-processed with custom filters, achieved 100% sensitivity and 77% precision on the optimized gene panel after excluding recurring artifacts. This level of performance may support clinical use with orthogonal confirmation of reportable CNVs, pending validation on laboratory-specific samples. Availability and implementation: The data underlying this article are available in the European Nucleo-tide Archive under project accession PRJEB87628.