vcfx
VCFX is a collection of specialized C/C++ command-line tools designed for efficient manipulation, analysis, and transformation of VCF files.
Science Score: 44.0%
This score indicates how likely this project is to be science-related based on various indicators:
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✓CITATION.cff file
Found CITATION.cff file -
✓codemeta.json file
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✓.zenodo.json file
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○DOI references
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○Academic publication links
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○Academic email domains
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (20.0%) to scientific vocabulary
Keywords
Repository
VCFX is a collection of specialized C/C++ command-line tools designed for efficient manipulation, analysis, and transformation of VCF files.
Basic Info
- Host: GitHub
- Owner: ieeta-pt
- License: mit
- Language: C++
- Default Branch: main
- Homepage: https://ieeta-pt.github.io/VCFX/
- Size: 6.17 MB
Statistics
- Stars: 1
- Watchers: 1
- Forks: 1
- Open Issues: 0
- Releases: 2
Topics
Metadata Files
README.md
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)
bash
pip install vcfx
After installing the Python bindings you can run any tool directly:
python
import vcfx
vcfx.run_tool("alignment_checker", "--help")
Bioconda
bash
conda install -c bioconda vcfx
Docker
bash
docker pull ghcr.io/jorgemfs/vcfx:latest
docker run --rm ghcr.io/jorgemfs/vcfx:latest VCFX_tool_name --help
Build from Source
bash
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
bash
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 toolspython/– optional Python bindingsdocs/– documentation sourcestests/– shell and Python testsexamples/– 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:
bash
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.
Owner
- Name: IEETA
- Login: ieeta-pt
- Kind: organization
- Website: www.ieeta.pt
- Repositories: 28
- Profile: https://github.com/ieeta-pt
Citation (CITATION.cff)
cff-version: 1.2.0
message: "If you use this software, please cite it."
title: "VCFX: A Minimalist, Modular Toolkit for Streamlined Variant Analysis"
version: "1.0.3"
authors:
- family-names: Silva
given-names: Jorge Miguel
- family-names: Oliveira
given-names: José Luis
date-released: "2025-01-01"
preferred-citation:
type: conference-paper
title: "VCFX: A Minimalist, Modular Toolkit for Streamlined Variant Analysis"
authors:
- family-names: Silva
given-names: Jorge Miguel
- family-names: Oliveira
given-names: José Luis
conference:
name: "12th International Work-Conference on Bioinformatics and Biomedical Engineering (IWBBIO 2025)"
year: "2025"
note: "Accepted for presentation; to appear in the IWBBIO 2025 proceedings."
GitHub Events
Total
- Issues event: 1
- Watch event: 2
- Push event: 12
- Pull request event: 3
- Fork event: 1
Last Year
- Issues event: 1
- Watch event: 2
- Push event: 12
- Pull request event: 3
- Fork event: 1
Packages
- Total packages: 1
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Total downloads:
- pypi 142 last-month
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 2
- Total maintainers: 1
pypi.org: vcfx
Python bindings for the VCFX toolkit - comprehensive VCF manipulation and analysis
- Homepage: https://github.com/ieeta-pt/VCFX
- Documentation: https://ieeta-pt.github.io/VCFX/
- License: mit
-
Latest release: 1.0.3
published 7 months ago
Rankings
Maintainers (1)
Dependencies
- actions/checkout v3 composite
- actions/setup-python v4 composite