CanSys is tool that quantifies the contributions of germline and somatic alterations to biological pathway-level disturbances in individual cancer samples. It annotates Variant Call Format (VCF) files with Combined Annotation Dependent Depletion (CADD) scores, calculates gene-level impact scores using CADD and Cancer Dependency Map (DepMap) scores, and maps affected genes onto biological pathways using specified databases (GO and KEGG). We also offer a web-based application cansysplot that allows users to analyze and interactively visualize pathway disturbances in networks. Additionally, the application facilitates the visualization of disturbance networks using data derived from The Cancer Genome Atlas (TCGA). If you use the CanSys tool in your research, please cite: Dai, J., Posta, M., Marczyk, M. et al. Functional germline variants together with somatic mutations alter the integrity of cancer hallmark regulatory networks. Genome Med (2026). https://doi.org/10.1186/s13073-026-01644-8