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 Homepage
• Manual
  • Installation Instructions.
• Docker Compose Installer.

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 >=3.8
  • 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.*