SVkhor: a unified framework for structural variant integration across long-read, short-read, and optical genome mapping data

SVkhor is a software framework designed to merge outputs from multiple structural variant detectors in human genome analysis and integrate them across short-read sequencing, long-read sequencing, and optical genome mapping technologies. Different technologies and detectors vary in breakpoint resolution, allele representation, variant annotation, and VCF file structure. SVkhor addresses these challenges through caller-aware normalization, within-technology merging, and cross-technology integration. The result is compact structural variant catalogs with source annotation suitable for benchmarking and further interpretation. Testing on the HG002 sample and analysis of a clinical trio demonstrated that SVkhor reduces redundant complexity at the detector level while preserving technology-specific evidence.