{"id":14970822,"url":"https://github.com/combat-tb/tbvcfreport","last_synced_at":"2026-02-24T21:33:59.042Z","repository":{"id":48945481,"uuid":"123902832","full_name":"COMBAT-TB/tbvcfreport","owner":"COMBAT-TB","description":"Generate an interactive HTML-based report from M.tb SnpEff annotated VCF(s)","archived":false,"fork":false,"pushed_at":"2024-06-07T11:02:56.000Z","size":1408,"stargazers_count":2,"open_issues_count":1,"forks_count":2,"subscribers_count":4,"default_branch":"main","last_synced_at":"2025-01-31T19:28:12.126Z","etag":null,"topics":["combat-tb-neodb","galaxy-project","neo4j","snpeff","tuberculosis","variant-annotations","vcf","vcf-files"],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/COMBAT-TB.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}},"created_at":"2018-03-05T10:22:48.000Z","updated_at":"2024-05-31T15:02:05.000Z","dependencies_parsed_at":"2024-06-07T12:34:00.147Z","dependency_job_id":"baa408b2-4351-44d9-b7fc-97698ddac68f","html_url":"https://github.com/COMBAT-TB/tbvcfreport","commit_stats":{"total_commits":124,"total_committers":2,"mean_commits":62.0,"dds":"0.32258064516129037","last_synced_commit":"0d3994295ed86bfee5372e4a43bb6b59cd4fe863"},"previous_names":[],"tags_count":22,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/COMBAT-TB%2Ftbvcfreport","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/COMBAT-TB%2Ftbvcfreport/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/COMBAT-TB%2Ftbvcfreport/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/COMBAT-TB%2Ftbvcfreport/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/COMBAT-TB","download_url":"https://codeload.github.com/COMBAT-TB/tbvcfreport/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":238337462,"owners_count":19455314,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","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":["combat-tb-neodb","galaxy-project","neo4j","snpeff","tuberculosis","variant-annotations","vcf","vcf-files"],"created_at":"2024-09-24T13:44:11.907Z","updated_at":"2025-10-26T13:31:31.784Z","avatar_url":"https://github.com/COMBAT-TB.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# **tbvcfreport**\n\n![tbvcfreport build status](https://github.com/COMBAT-TB/tbvcfreport/actions/workflows/tbvcfreport.yaml/badge.svg)\n[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/tbvcfreport/README.html)\n\nGenerate an interactive HTML-based report from *M.tb* SnpEff annotated VCF(s) with links to the [COMBAT-TB-eXplorer](https://explorer.sanbi.ac.za/).\n\n![test-report-img](img/test-report.png)\n\n## Usage\n\n**Prerequisites:**\n\n- [SnpEff](http://snpeff.sourceforge.net/SnpEff_manual.html) annotated *M.tuberculosis* VCF file(s).\n\n**Optional:**\n- A [COMBAT-TB-NeoDB](https://github.com/COMBAT-TB/combat-tb-neodb) instance, `tbvcfreport` defaults to [neodb.sanbi.ac.za](https://neodb.sanbi.ac.za).\n  - See [documentation](https://github.com/COMBAT-TB/combat-tb-neodb) if you want a local installation and `export DATABASE_URI=localhost` for `tbvcfreport` to use your local instance.\n\n### Installation\n\n#### Using `pip`\n\n```sh\n$ pip install -i https://test.pypi.org/simple/ tbvcfreport\n...\n```\n\n#### Using `conda`\n\nWith an activated [Bioconda](https://bioconda.github.io/) channel:\n\n```sh\n$ conda install tbvcfreport\n...\n```\n\n#### From source\n\n```sh\n$ git clone https://github.com/COMBAT-TB/tbvcfreport.git\n...\n$ cd tbvcfreport\n$ virtualenv envname\n$ source envname/bin/activate\n$ pip install -r requirements.txt\n$ pip install -e .\n```\n\n### Run `tbvcfreport`\n\n```sh\n$ tbvcfreport --help\nUsage: tbvcfreport [OPTIONS] COMMAND [ARGS]...\n\n  Generate an HTML-based VCF report from SnpEff annotated VCF file(s).\n\nOptions:\n  --help  Show this message and exit.\n\nCommands:\n  generate  Generate an interactive HTML-based VCF report.\n\n```\n\n```sh\n$ tbvcfreport generate --help\nUsage: tbvcfreport generate [OPTIONS] VCF_DIR\n\n  Generate an interactive HTML-based VCF report.\n\nOptions:\n  -t, --tbprofiler-report FILENAME\n                                  TBProfiler json report.\n  -f, --filter-udi / -nf, --no-filter-udi\n                                  Filter upstream, downstream and intergenic\n                                  variants.  [default: True]\n  --help                          Show this message and exit.\n\n```\n\n```sh\n$ tbvcfreport generate VCF_DIR/\nProcessing...\n```\n\nThis will generate a `{vcf-file-name}.html` file in the current working directory (`pwd`).\n\n## In Galaxy\n\nWe have also added `tbvcfreport` to the [Galaxy](https://github.com/galaxyproject) [Tool Shed](https://toolshed.g2.bx.psu.edu/repository?repository_id=47a4512ab5a77049).\n\nKindly see [`this repository`](https://toolshed.g2.bx.psu.edu/repository?repository_id=47a4512ab5a77049) for the latest revision.\n\n![Galaxy-tbvcfreport](img/tbvcfreportgalaxy.png)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcombat-tb%2Ftbvcfreport","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fcombat-tb%2Ftbvcfreport","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcombat-tb%2Ftbvcfreport/lists"}