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Documentation Status https://app.codacy.com/project/badge/Grade/f47216cf5a4349acbb9baf5ca1c91329 https://app.codacy.com/project/badge/Coverage/f47216cf5a4349acbb9baf5ca1c91329 https://coveralls.io/repos/github/bihealth/varfish-server/badge.svg?branch=main

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. https://doi.org/10.1093/nar/gkaa241.

Getting Started

VarFish Repositories

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.

At a Glance

  • License: MIT
  • Dependencies / Tech Stack
    • Python >=3.7
    • 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.*.* 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.*.* 20210728 v0.3.*