{"id":38967295,"url":"https://github.com/bigbio/hvantk","last_synced_at":"2026-01-17T16:32:01.828Z","repository":{"id":222561848,"uuid":"751858635","full_name":"bigbio/hvantk","owner":"bigbio","description":"Hail variant annotation toolkit","archived":false,"fork":false,"pushed_at":"2026-01-13T20:57:14.000Z","size":38320,"stargazers_count":0,"open_issues_count":6,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2026-01-13T21:34:20.388Z","etag":null,"topics":["big-data","bigdata","genomics","hail","variant-analysis"],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/bigbio.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2024-02-02T13:38:01.000Z","updated_at":"2026-01-13T20:57:20.000Z","dependencies_parsed_at":"2025-03-28T14:26:10.922Z","dependency_job_id":"90efa996-5029-4bc2-b69c-e339e20d7203","html_url":"https://github.com/bigbio/hvantk","commit_stats":null,"previous_names":["enriquea/pyvatk","bigbio/hvantk"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/bigbio/hvantk","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bigbio%2Fhvantk","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bigbio%2Fhvantk/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bigbio%2Fhvantk/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bigbio%2Fhvantk/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/bigbio","download_url":"https://codeload.github.com/bigbio/hvantk/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bigbio%2Fhvantk/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28511867,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-17T13:38:16.342Z","status":"ssl_error","status_checked_at":"2026-01-17T13:37:44.060Z","response_time":85,"last_error":"SSL_read: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["big-data","bigdata","genomics","hail","variant-analysis"],"created_at":"2026-01-17T16:32:01.688Z","updated_at":"2026-01-17T16:32:01.804Z","avatar_url":"https://github.com/bigbio.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"[![Python Package using Conda](https://github.com/bigbio/hvantk/actions/workflows/python-package-conda.yml/badge.svg)](https://github.com/bigbio/hvantk/actions/workflows/python-package-conda.yml)\n[![Python application](https://github.com/bigbio/hvantk/actions/workflows/python-app.yml/badge.svg)](https://github.com/bigbio/hvantk/actions/workflows/python-app.yml)\n\n# hvantk\n\n**Hail-based toolkit for multiomics variant annotation and analysis.**\n\n`hvantk` is a modular toolkit that uses [Apache Hail](https://hail.is/) 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.\n\n**Core Capabilities:**\n- Variant annotations (ClinVar, dbNSFP, gnomAD, CCR scores)\n- Gene annotations (Ensembl, GeVIR, gene constraints)\n- Protein annotations (INSIDER protein-protein interactions)\n- Expression data (bulk \u0026 single-cell RNA-seq from UCSC, GTEx)\n- Joint genotyping workflows (GVCF combining, QC, format conversion)\n- Recipe-based batch processing\n\n## Installation\n\n```bash\ngit clone https://github.com/bigbio/hvantk\ncd hvantk\npoetry install\npoetry shell\n```\n\n### Using pip\n\n```bash\ngit clone https://github.com/bigbio/hvantk\ncd hvantk\npip install -e .\n```\n\n**Prerequisites**: Python ≥3.10, Apache Hail\n\n## Main Tools\n\n### HGC: Joint Genotyping Pipeline\n\nHigh-performance joint genotyping for large cohorts using Hail. Combines thousands of GVCF files with integrated quality control.\n\n**Key features:**\n- GVCF combination at scale\n- VDS ↔ MatrixTable ↔ VCF format conversion\n- Comprehensive QC metrics and visualization\n- Professional HTML QC reports\n\n**Quick example:**\n```bash\n# Combine GVCF files\nhvantk hgc gvcf-combine -g /data/gvcfs -o cohort.vds\n\n# Convert to MatrixTable and run QC\nhvantk hgc vds2mt -i cohort.vds -o cohort.mt\nhvantk hgc compute-qc -i cohort.mt -o cohort_qc.mt\n\n# Generate QC report\nhvantk hgc qc-report -i cohort_qc.mt -o qc_report.html\n```\n\n📖 **[Full HGC Documentation](docs/tools/hgc.md)**\n\n### Annotation Tables: Build Custom Annotation Resources\n\nCreate Hail Tables from public annotation databases (ClinVar, gnomAD, Ensembl, etc.).\n\n**Single table creation:**\n```bash\n# Build ClinVar annotation table\nhvantk mktable clinvar --raw-input clinvar.vcf.bgz --output-ht clinvar.ht --ref-genome GRCh38\n\n# Build Ensembl gene table\nhvantk mktable ensembl-gene --raw-input biomart.tsv.bgz --output-ht ensembl.ht\n```\n\n**Batch processing with recipes:**\n```bash\nhvantk mktable-batch --recipe tables_recipe.json\n```\n\n📖 **[Annotation Tables Guide](docs/library/usage.md#1-build-a-single-annotation-table-ht)**\n\n### Expression Matrices: Process Omics Data\n\nBuild Hail MatrixTables from bulk and single-cell expression data.\n\n**Example:**\n```bash\n# Convert UCSC Cell Browser data to MatrixTable\nhvantk mkmatrix ucsc -e expr.tsv.bgz -m metadata.tsv -o ucsc.mt\n\n# Batch processing\nhvantk mkmatrix-batch --recipe matrices_recipe.json\n```\n\n📖 **[Expression Data Guide](docs/library/usage.md#3-build-a-single-matrixtable-mt)**\n\n### Data Downloaders\n\nDownload curated datasets directly from public repositories.\n\n**Example:**\n```bash\n# Download UCSC Cell Browser dataset\nhvantk ucsc-downloader --dataset adultPancreas --output-dir data/ucsc\n```\n\n📖 **[Data Sources](docs/library/annotation-sources.md)**\n\n## Quick Start Example\n\n```bash\n# 1. Download a dataset\nhvantk ucsc-downloader --dataset adultPancreas --output-dir data/ucsc\n\n# 2. Convert to Hail MatrixTable\nhvantk mkmatrix ucsc \\\n  -e data/ucsc/exprMatrix.tsv.bgz \\\n  -m data/ucsc/meta.tsv \\\n  -o data/ucsc/adultPancreas.mt\n\n# 3. Build annotation tables via recipe\ncat \u003e recipe.json \u003c\u003c EOF\n{\n  \"tables\": [\n    {\n      \"name\": \"clinvar\",\n      \"input\": \"/data/clinvar.vcf.bgz\",\n      \"output\": \"/out/clinvar.ht\",\n      \"params\": {\"reference_genome\": \"GRCh38\"}\n    }\n  ]\n}\nEOF\n\nhvantk mktable-batch --recipe recipe.json\n```\n\n## Documentation\n\n- **[Architecture Overview](docs/ARCHITECTURE.md)** - Module organization and design patterns\n- **[Usage Guide](docs/library/usage.md)** - Detailed usage examples and recipes\n- **[Data Sources](docs/library/annotation-sources.md)** - Available annotation sources and download instructions\n- **[HGC Tool](docs/tools/hgc.md)** - Joint genotyping and quality control\n- **[API Reference](docs/ARCHITECTURE.md#extension-points)** - Extending hvantk with custom builders\n- **[Full Documentation Index](docs/README.md)** - Complete documentation structure\n\n## Citation\n\nIf you use hvantk in your research, please cite:\n\n```bibtex\n@software{hvantk2024,\n  title = {hvantk: Hail-based toolkit for multi-omics variant annotation and analysis},\n  author = {Perez-Riverol, Yasset and Audain, Enrique},\n  year = {2024},\n  url = {https://github.com/bigbio/hvantk}\n}\n```\n\n## Contributing\n\nWe welcome contributions! Please see [CONTRIBUTING.md](CONTRIBUTING.md) for detailed information on:\n- Development workflow and setup\n- Adding new data sources\n- Code style guidelines\n- Testing requirements\n- Pull request process\n\n**Developer quick start:**\n```bash\npoetry install\npytest -q\nhvantk --help\n```\n\n## License\n\nThis project is licensed under the MIT License - see the [LICENSE](LICENSE) file for details.\n\n## Support\n\n- **Issues**: [GitHub Issues](https://github.com/bigbio/hvantk/issues)\n- **Questions**: Open a discussion on GitHub\n- **Documentation**: [docs/](docs/)\n\n## Acknowledgments\n\n- Built on [Apache Hail](https://hail.is/) for distributed genomic data processing\n- Integrates data from ClinVar, gnomAD, Ensembl, UCSC, and other public resources\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbigbio%2Fhvantk","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbigbio%2Fhvantk","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbigbio%2Fhvantk/lists"}