{"id":24998423,"url":"https://github.com/cameronraysmith/vep-example-usage","last_synced_at":"2026-01-07T16:52:22.644Z","repository":{"id":232628692,"uuid":"698485853","full_name":"cameronraysmith/vep-example-usage","owner":"cameronraysmith","description":"example usage of ensembl vep","archived":false,"fork":false,"pushed_at":"2023-09-30T04:19:40.000Z","size":14,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":2,"default_branch":"main","last_synced_at":"2025-02-04T17:58:03.513Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","language":"HTML","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/cameronraysmith.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"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}},"created_at":"2023-09-30T04:19:36.000Z","updated_at":"2023-09-30T04:26:10.000Z","dependencies_parsed_at":"2024-04-10T19:14:09.029Z","dependency_job_id":"95524594-d7cc-4256-a8a0-3ceba73c03d4","html_url":"https://github.com/cameronraysmith/vep-example-usage","commit_stats":null,"previous_names":["cameronraysmith/vep-example-usage"],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cameronraysmith%2Fvep-example-usage","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cameronraysmith%2Fvep-example-usage/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cameronraysmith%2Fvep-example-usage/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cameronraysmith%2Fvep-example-usage/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/cameronraysmith","download_url":"https://codeload.github.com/cameronraysmith/vep-example-usage/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":246215826,"owners_count":20741894,"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":[],"created_at":"2025-02-04T17:58:09.040Z","updated_at":"2026-01-07T16:52:22.592Z","avatar_url":"https://github.com/cameronraysmith.png","language":"HTML","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Ensembl VEP (Variant Effect Predictor) example usage\n\nThis repository provides example usage of the [Ensembl Variant Effect Predictor](https://ensembl.org/info/docs/tools/vep/script/index.html) (VEP) ([src](https://github.com/Ensembl/ensembl-vep)) in both online and offline modes in the [official container image](https://hub.docker.com/r/ensemblorg/ensembl-vep).\n\n### Prerequisites\n\n1. [Docker](https://www.docker.com/products/docker-desktop) and [Docker Compose](https://docs.docker.com/compose/install/) installed.\n2. [aria2c](https://aria2.github.io/) or [wget](https://www.gnu.org/software/wget/) for downloading data. The script will use `aria2c` if available, otherwise it will fall back to `wget`. The former reduces download time from 9 hours to 30 minutes for the 20GB cache.\n\n### Directory Structure\n\nBefore running, ensure you have the following directory structure:\n\n```\n.\n├── cache/  # VEP cache files will be stored here.\n├── data/   # Your input data, i.e., rsids.txt should be placed here.\n├── output/ # VEP results will be saved here.\n├── vep.sh\n└── docker-compose.yml\n```\n\n### Running VEP\n\n1. Ensure `vep.sh` is executable:\n\n   ```bash\n   chmod +x vep.sh\n   ```\n\n2. You can run VEP in online mode (default) directly using:\n\n   ```bash\n   ./vep.sh\n   ```\n\n   To run in offline mode (utilizing local cache), set the `VEP_MODE` environment variable to \"offline\":\n\n   ```bash\n   VEP_MODE=offline ./vep.sh\n   ```\n\n   In offline mode, the script will first check if the VEP cache is available in the `cache/` directory. If not, it will download the cache files and extract them there.\n   This is about 20GB and will take 30 minutes with aria2c or 9 hours with wget.\n\n3. The output will be saved in the `output/` directory as `vep_output.txt`.\n\n### Customizing the Input\n\nTo analyze a different set of variants:\n\n1. Place your input file, such as `rsids.txt`, into the `data/` directory.\n2. Modify the `input_file` path in the `docker-compose.yml` under the `command` section accordingly.\n\n### Notes\n\n- The Docker setup uses the official Ensembl VEP Docker image.\n- Volumes are used to map local directories (`cache`, `data`, and `output`) to directories within the Docker container.\n- The `docker-compose.yml` file specifies the Docker configurations and the commands to run VEP based on the mode (online/offline).\n\n### Troubleshooting\n\n- If you encounter issues with file permissions, check that your current user has appropriate permissions to read/write to the `cache`, `data`, and `output` directories.\n- Ensure your input files are correctly formatted and placed in the `data/` directory before running the script.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcameronraysmith%2Fvep-example-usage","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fcameronraysmith%2Fvep-example-usage","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcameronraysmith%2Fvep-example-usage/lists"}