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. https://doi.org/10.1093/nar/gkaa241.
- varfish-server The VarFish Server is the web frontend used by the end users / data analysts.
- 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 The VarFish Command Line Interface allows to import data through the VarFish REST API.
- varfish-db-downloader The VarFish DB Downloader is a command line tool for downloading the background database.
- 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.
- 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.
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 |
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.* |