Overview
Varan is a Python-based application that provides a pipeline to prepare and manipulate cancer genomics data for cBioPortal.
Features
- Study Creation: Generates a validated study folder from raw VCF files, ready for upload to cBioPortal.
- Study Manipulation: Enables study modification by merging studies or extracting/removing samples.
Quick Start
Deploy Varan from synthetic raw data to analysis pipelines in under 30 minutes using a Docker container.
User Guide
Detailed descriptions of Varan's usage, functions, and workflows.
Issue Reporting
Open an issue on GitHub if you encounter problems not covered in the documentation.
Citing Varan
If you use this tool in your research, please cite:
Parrillo C., Kulesko M., Persiani F., De Marco L., Petescia P., Mastrantoni L., Nero C., Minucci A., Giacò L. Varan: a tool for managing mutational data and creating cancer studies in cBioPortal. NAR Genomics and Bioinformatics, 2025.
https://doi.org/10.1093/nargab/lqaf107
⚠️ Varan is intended for research use only and not for patient treatment, diagnosis and/or medical records.