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VarFish

VarFish is a user-friendly web application for the quality control, filtering, prioritization, analysis, and user-based annotation of DNA variant data with a focus on rare disease genetics. It is capable of processing variant call files with single or multiple samples. ...

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Description

VarFish is a user-friendly web application for the quality control, filtering, prioritization, analysis, and user-based annotation of DNA variant data with a focus on rare disease genetics. It is capable of processing variant call files with single or multiple samples. The variants are automatically annotated with population frequencies, molecular impact, and presence in databases such as ClinVar. Further, it provides support for pathogenicity scores including CADD, MutationTaster, and phenotypic similarity scores. Users can filter variants based on these annotations and presumed inheritance pattern and sort the results by these scores. Variants passing the filter are listed with their annotations and many useful link-outs to genome browsers, other gene/variant data portals, and external tools for variant assessment. VarFish allows users to create their own annotations including support for variant assessment following ACMG-AMP guidelines. In close collaboration with medical practitioners, VarFish was designed for variant analysis and prioritization in diagnostic and research settings as described in the software's extensive manual. The user interface has been optimized for supporting these protocols. Users can install VarFish on their own in-house servers where it provides additional lab notebook features for collaborative analysis and allows re-analysis of cases, e.g. after update of genotype or phenotype databases.

Logo of VarFish
Keywords
Annotation
Data analysis
Health
python
Programming languages
  • Python 73%
  • Vue 11%
  • TypeScript 10%
  • JavaScript 3%
  • HTML 2%
  • Other 1%
License
  • MIT
</>Source code

Participating organisations

Max Delbrück Center for Molecular Medicine
Berlin Institute of Health at Charité - Universitätsmedizin Berlin

Reference papers

Mentions

Contributors

DB
Dieter Beule
Last author
Berlin Institute of Health at Charité - Universitätsmedizin Berlin
MH
Manuel Holtgrewe
OS
Oliver Stolpe
MN
Mikko Nieminen
SM
Stefan Mundlos
AK
Alexej Knaus
UK
Uwe Kornak
DS
Dominik Seelow
LS
Lara Segebrecht
MS
Malte Spielmann
BF
Björn Fischer-Zirnsak
FB
Felix Boschann