hvantk

Hail-based toolkit for multiomics variant annotation and analysis.

hvantk is a modular toolkit that uses Hail to annotate and analyze variants, genes, proteins, and expression data from heterogeneous omics sources. The library enables multiomics integration to improve the interpretation of genetic variants.

Installation

git clone https://github.com/bigbio/hvantk
cd hvantk
poetry install
eval "$(poetry env activate)"

Prerequisites: Python >=3.10, Hail

Verify it works:

hvantk utils check-install
hvantk --help

Toolkit

Tool	Description	Command	Docs
Downloads	Acquire external datasets (ClinVar, ClinGen, HGNC, etc.)	hvantk download <source>	Data Sources
Annotation builders	Variant, gene, and protein tables (ClinVar, dbNSFP, gnomAD, Ensembl, HGNC, INSIDER, CCR)	hvantk mktable <source>	Usage Guide
Expression builders	Bulk and single-cell matrices (UCSC, GTEx, Expression Atlas, CPTAC)	hvantk mkmatrix <source>	Usage Guide
Batch recipes	Recipe-based batch processing for tables and matrices	hvantk mktable-batch	Recipes
HGC	Joint genotyping pipeline (GVCF combining, QC, format conversion)	hvantk hgc	HGC
Ancestry	Ancestry inference (PCA + Random Forest classification)	hvantk ancestry-inference	Ancestry
QTL Cascade	Molecular QTL integration (eQTL + pQTL cascade, colocalization ABF)	hvantk qtlcascade	QTL Cascade
EnrichEx	Gene set enrichment (overlap testing + rare variant burden)	hvantk enrichex	EnrichEx
PS-ROC	Pathogenicity score ROC evaluation against ClinVar labels	hvantk psroc	PS-ROC
PTM	Post-translational modification variant classification	hvantk ptm	PTM
Expression	Expression analysis (summarize, marker extraction)	hvantk expression	Usage Guide

Documentation

Full docs site: https://bigbio.github.io/hvantk

• Data Sources -- Available annotations and how to acquire them
• Examples -- Tutorials and walkthroughs for each tool
• Architecture -- Design patterns and extension points

Citation

If you use hvantk in your research, please cite:

@software{hvantk2024,
  title = {hvantk: Hail-based toolkit for multi-omics variant annotation and analysis},
  author = {Perez-Riverol, Yasset and Audain, Enrique},
  year = {2024},
  url = {https://github.com/bigbio/hvantk}
}

Contributing

See CONTRIBUTING.md for development workflow, code style, and testing requirements.

poetry install
pytest -q
hvantk --help

License

MIT License - see LICENSE.

Support

• GitHub Issues
• Documentation