CNAG Biomedical Informatics framework for variant calling
CBIcall (CNAG Biomedical Informatics framework for variant calling) is a configuration-driven workflow dispatcher for Illumina sequencing variant calling, designed to support reproducible, auditable, and consistent execution of analysis pipelines in production environments.
📘 Documentation: https://cnag-biomedical-informatics.github.io/cbicall
🐳 Docker Hub Image: https://hub.docker.com/r/manuelrueda/cbicall/tags
- Installation
- Non-Containerized
- Containerized
- Quick Start
- Documentation
- Citation
- License
CBIcall orchestrates germline variant calling workflows for Illumina sequencing data. It does not implement variant calling algorithms itself. Instead, it validates parameters, resolves workflows from a versioned registry, dispatches curated Bash or Snakemake pipelines, and captures logs and structured metadata for traceability.
Key points:
- Configuration-driven execution from a YAML parameter file
- Curated Bash and Snakemake workflow support
- Support for WES, WGS, and mtDNA analysis modes
- Structured run logging and traceable runtime metadata
- Optional partial workflow starts for supported engines
bin/cbicall -p params.yaml -t 8
Runnable examples and sample inputs are available under examples/.
The full technical reference lives in the documentation site and repository docs:
- General usage and parameter reference: docs/usage/usage.md
- Quick start: docs/usage/quickstart.md
- End-to-end examples: docs/usage/end-to-end-example-wes.md, docs/usage/end-to-end-example-mit.md
- Technical details: docs/technical-details/architecture.md
CBIcall: a configuration-driven framework for variant calling in large sequencing cohorts. Preprint DOI.
Written by Manuel Rueda (mrueda). GitHub repository: https://github.com/CNAG-Biomedical-Informatics/cbicall.
Please see the included LICENSE file for distribution and usage terms.