SVkhor: a unified framework for structural variant integration across long-read, short-read, and optical genome mapping data
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Summary
Multi-technology human genome structural variant (SV) discovery is challenged by differences in breakpoint resolution, allele representation, SV annotation, and VCF structure across various callers and platforms. Here, we present SVkhor, a software framework designed to merge outputs from multiple callers within each technology and integrate SV callsets across available short-read sequencing, long-read sequencing, and optical genome mapping data. SVkhor addresses these challenges through caller-aware normalization, within-technology merging, and cross-technology integration, producing compact, source-annotated SV catalogs suitable for benchmarking and downstream interpretation. Benchmarking using HG002 and analysis of a clinical trio demonstrate that SVkhor reduces redundant caller-level complexity while preserving technology-specific evidence, enabling the transition from heterogeneous SV callsets to interpretable sample- and family-level SV catalogs.
Availability and implementation
SVkhor is implemented as a Linux command-line workflow. The source code, documentation, and example workflows are accessible at http://gitlab.gad-bioinfo.org/gad-public/svkhor under the MIT license.
Contact
Antonio.Vitobello@u-bourgogne.fr or yannis.duffourd@u-bourgogne.fr
Supplementary information
Supplementary data are accessible online.
