{"id":18961613,"url":"https://github.com/combat-tb/vcf2neo","last_synced_at":"2025-04-19T11:41:05.902Z","repository":{"id":55131523,"uuid":"78718939","full_name":"COMBAT-TB/vcf2neo","owner":"COMBAT-TB","description":"A tool to import SnpEff annotated files to a Neo4j Graph database","archived":false,"fork":false,"pushed_at":"2022-12-08T05:10:46.000Z","size":39992,"stargazers_count":3,"open_issues_count":3,"forks_count":2,"subscribers_count":7,"default_branch":"master","last_synced_at":"2025-03-29T07:22:41.088Z","etag":null,"topics":["graph-database","neo4j-database","py2neo","snpeff","tuberculosis","variant-calling"],"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}},"created_at":"2017-01-12T07:13:50.000Z","updated_at":"2022-05-20T10:59:11.000Z","dependencies_parsed_at":"2023-01-24T12:00:15.504Z","dependency_job_id":null,"html_url":"https://github.com/COMBAT-TB/vcf2neo","commit_stats":null,"previous_names":[],"tags_count":9,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/COMBAT-TB%2Fvcf2neo","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/COMBAT-TB%2Fvcf2neo/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/COMBAT-TB%2Fvcf2neo/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/COMBAT-TB%2Fvcf2neo/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/COMBAT-TB","download_url":"https://codeload.github.com/COMBAT-TB/vcf2neo/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":249195411,"owners_count":21228193,"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":["graph-database","neo4j-database","py2neo","snpeff","tuberculosis","variant-calling"],"created_at":"2024-11-08T14:13:46.493Z","updated_at":"2025-04-16T04:32:53.618Z","avatar_url":"https://github.com/COMBAT-TB.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# vcf2neo\n\n[![Build Status](https://travis-ci.org/COMBAT-TB/vcf2neo.svg?branch=master)](https://travis-ci.org/COMBAT-TB/vcf2neo)\n[![Coverage Status](https://coveralls.io/repos/github/COMBAT-TB/vcf2neo/badge.svg?branch=master)](https://coveralls.io/github/COMBAT-TB/vcf2neo?branch=master)\n[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.1219127.svg)](https://doi.org/10.5281/zenodo.1219127)\n\nA tool to import and map **[SnpEff annotated](http://snpeff.sourceforge.net/SnpEff.html)** VCF files to [COMBAT-TB NeoDB](https://github.com/COMBAT-TB/combat-tb-neodb) Graph database.\n\n**Prerequisites**:\n\n- [`docker`](https://docs.docker.com/v17.12/install/) and [`docker-compose`](https://docs.docker.com/compose/install/) :whale:\n\n## Usage\n\n**Clone repository**:\n\n```sh\n$ git clone https://github.com/SANBI-SA/vcf2neo.git\n...\n$ cd vcf2neo\n```\n\n**Build [COMBAT-TB NeoDB](https://github.com/COMBAT-TB/combat-tb-neodb)**:\n\n```sh\n$ docker-compose up --build -d\n...\n```\n\n**Install and run `vcf2neo`**:\n\n- Using `pip`\n\n```sh\n$ pip install -i https://test.pypi.org/simple/ vcf2neo\n...\n```\n\n- or via `setup` in `virtualenv`\n\n```sh\n$ virtualenv envname\n...\n$ source envname/bin/activate\n$ pip install -r requirements.txt\n$ python setup.py install\n```\n\n**Import and map SnpEff annotated VCF files to genes and drugs in NeoDB**:\n\nYou change the default database location (`localhost`) by setting the\n`DATABASE_URL` environment variable to `remote`.\n\n```sh\n$ vcf2neo load_vcf --help\nUsage: vcf2neo load_vcf [OPTIONS] VCF_DIR\n\n  Load SnpEff annotated VCF files to genes and drugs in NeoDb.\n\nOptions:\n  --owner TEXT                    Specify owner.  [default: $USER; required]\n  -p, --phenotype [XDR|MDR|SUSCEPTIBLE|UNKNOWN]\n                                  Specify phenotype.  [required]\n  -a, --antibiotic TEXT           Specify antibiotic. E.g. Rifampicin\n                                  [required]\n  --help                          Show this message and exit.\n```\n\n```sh\n$ vcf2neo load_vcf -p UNKNOWN -a UNKNOWN PATH/TO/VCF_DIR\n...\n```\n\n**Exploring variant data**:\n\nPoint your browser to [localhost:7474](http://0.0.0.0:7474) to access the Neo4j browser.\n\nTo view the schema, run:\n\n```cql\ncall db.schema.visualization\n```\n\nSample [Cypher](https://neo4j.com/developer/cypher-query-language/) query:\n\n```cql\nMATCH(g:Gene)--(v:Variant)--(cs:CallSet)\nRETURN g.name as gene, v.consequence as variant, cs.name as file\nLIMIT 25\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcombat-tb%2Fvcf2neo","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fcombat-tb%2Fvcf2neo","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcombat-tb%2Fvcf2neo/lists"}