VCFX: Comprehensive VCF Manipulation Toolkit

VCFX is a set of small C/C++ command line tools for manipulating and analysing Variant Call Format (VCF) files. Each tool does one job well and they can be chained together using standard streams.

Features

• 60+ Specialized Tools for filtering, transforming and analysing variants
• Pipeline Ready: tools read from stdin and write to stdout
• Fast: designed for large genomic datasets
• Cross Platform: Linux and macOS support
• WebAssembly Builds for browser or Node.js usage
• Easy Installation via PyPI, Bioconda or Docker
• Python Bindings for programmatic access

Installation

PyPI (Python Package)

pip install vcfx

After installing the Python bindings you can run any tool directly:

import vcfx
vcfx.run_tool("alignment_checker", "--help")

Bioconda

conda install -c bioconda vcfx

Docker

docker pull ghcr.io/jorgemfs/vcfx:latest
docker run --rm ghcr.io/jorgemfs/vcfx:latest VCFX_tool_name --help

Build from Source

git clone https://github.com/ieeta-pt/VCFX.git
cd VCFX
mkdir build && cd build
cmake .. -DPYTHON_BINDINGS=ON
make

Optionally run make install to place the tools in ~/.local/bin.

Quick Example

cat input.vcf | \
  VCFX_variant_classifier --append-info | \
  grep 'VCF_CLASS=SNP' | \
  VCFX_allele_freq_calc > snp_frequencies.tsv

Documentation

Full documentation is available at ieeta-pt.github.io/VCFX. The docs folder contains the sources and can be served locally with mkdocs serve.

Repository Layout

• src/ – C++ source code for all tools
• python/ – optional Python bindings
• docs/ – documentation sources
• tests/ – shell and Python tests
• examples/ – usage examples and workflows

Development

Run tests with pytest and ctest from the build directory. Code style is enforced with clang-format and pre-commit hooks:

pre-commit install

Citation

If you use VCFX in your research please cite:

@inproceedings{silva2025vcfx,
  title={VCFX: A Minimalist, Modular Toolkit for Streamlined Variant Analysis},
  author={Silva, Jorge Miguel and Oliveira, José Luis},
  booktitle={12th International Work-Conference on Bioinformatics and Biomedical Engineering (IWBBIO 2025)},
  year={2025},
  organization={Springer}
}

License

VCFX is distributed under the MIT License.