https://github.com/varfish-org/varfish-server
VarFish: comprehensive DNA variant analysis for diagnostics and research
https://github.com/varfish-org/varfish-server
genetics varfish variant-filtration variant-prioritization vcf
Last synced: 2 months ago
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VarFish: comprehensive DNA variant analysis for diagnostics and research
- Host: GitHub
- URL: https://github.com/varfish-org/varfish-server
- Owner: varfish-org
- License: mit
- Created: 2019-06-05T06:57:33.000Z (almost 7 years ago)
- Default Branch: main
- Last Pushed: 2026-02-02T05:34:21.000Z (3 months ago)
- Last Synced: 2026-02-02T17:12:34.647Z (3 months ago)
- Topics: genetics, varfish, variant-filtration, variant-prioritization, vcf
- Language: Python
- Homepage:
- Size: 62 MB
- Stars: 52
- Watchers: 2
- Forks: 12
- Open Issues: 200
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- License: LICENSE
- Security: SECURITY.rst
Awesome Lists containing this project
README
[](https://varfish-server.readthedocs.io/en/latest/?badge=latest)
[](https://codecov.io/gh/varfish-org/varfish-server)
[](https://opensource.org/licenses/MIT)
# VarFish
**Comprehensive DNA variant analysis for diagnostics and research.**
This is the repository for the web server component.
Holtgrewe, M.; Stolpe, O.; Nieminen, M.; Mundlos, S.; Knaus, A.; Kornak, U.; Seelow, D.; Segebrecht, L.; Spielmann, M.; Fischer-Zirnsak, B.; Boschann, F.; Scholl, U.; Ehmke, N.; Beule, D. *VarFish: Comprehensive DNA Variant Analysis for Diagnostics and Research*. Nucleic Acids Research 2020, gkaa241. .
## Getting Started
- [VarFish Homepage](https://www.cubi.bihealth.org/software/varfish/)
- [Manual](https://varfish-server.readthedocs.io/en/latest/)
- [Installation Instructions](https://varfish-server.readthedocs.io/en/latest/admin_install.html).
- [Docker Compose Installer](https://github.com/varfish-org/varfish-docker-compose#run-varfish-server-using-docker-compose).
## VarFish Repositories
- [varfish-server](https://github.com/varfish-org/varfish-server) The VarFish Server is the web frontend used by the end users / data analysts.
- [varfish-annotator](https://github.com/varfish-org/varfish-annotator) The VarFish Annotator is a command line utility used for annotating VCF files and converting them to files that can be imported into VarFish Server.
- [varfish-cli](https://github.com/varfish-org/varfish-cli) The VarFish Command Line Interface allows to import data through the VarFish REST API.
- [varfish-db-downloader](https://github.com/varfish-org/varfish-db-downloader) The VarFish DB Downloader is a command line tool for downloading the background database.
- [varfish-docker-compose](https://github.com/varfish-org/varfish-docker-compose) Quickly get started running a VarFish server by using Docker Compose. We provide a prebuilt data set with some already imported data.
## At a Glance
- License: MIT
- Dependencies / Tech Stack
- Python \>=3.8
- Django 3
- PostgreSQL \>=12
GitHub is used for public issue tracking. Currently, development happens
on internal infrastructure.
## VarFish Component Compatibility Table
The following combinations have been validated / are supported to work.
| VarFish Server | VarFish CLI | VarFish Annotator |
| -------------- | ----------- | ----------------- |
| v1.2.2 | v0.3.0 | v0.21 |
| v1.2.1 | v0.3.0 | v0.21 |
| v1.2.0 | v0.3.0 | v0.21 |
## VarFish Data Release Compatibility Table
The following combinations have been validated / are supported to work.
| VarFish Server | Data Release | VarFish DB Downloader |
| -------------- | ------------ | --------------------- |
| v1.2.2 | 20210728c | v0.3.\* |
| v1.2.1 | 20210728 | v0.3.\* |
| v1.2.1 | 20210728b | v0.3.\* |
| v1.2.0 | 20210728 | v0.3.\* |
| v1.2.0 | 20210728b | v0.3.\* |