Genomic variants explorer
Varapp is an application to filter genetic variants, with a reactive graphical user interface.
The application has been developed in a collaboration between the Swiss Institute of Bioinformatics (SIB) and the Lausanne University hospital (CHUV).
The complete documentation is available at https://varapp-demo.vital-it.ch/docs/ .
Common filtering pipelines can be very tedious, including an annotation step, complicated forms, multiple exports to spreadsheets, merging and manual curation of theses spreadsheets. Although there already exist several tools to facilitate the annotation of lists of variants and apply basic filters such as frequency in a population, quality or location, Varapp has at least one of the following advantages over existing software:
Varapp is typically well-suited to cover the following two use cases, the result of which is obtained within a few seconds:
We consider all variants in the exomes of one or several families affected by the same hereditary disease. We are searching for the variants that are susceptible to cause the disease.
Varapp provides one-click filters for dominant, recessive, de novo, X-linked, and compound heterozygous cases.
We consider the same few genes (typically a few hundred) in a large series of independent individuals. We seek rare variants with strong impact, then inspect the individual(s) that carry them.
… a variants caller:
It starts after the variant calling has already been done, and works based on the VCF file that the latter produces.
… adapted to full genome sequencing or million genomes projects:
For the moment, the app is responsive with datasets up to 500‘000 variants and a few hundred individuals, but performance issues are expected when dealing with millions of variants, as in the case of full genome sequencing, or with thousands of samples.
One demo version of the program is available at https://varapp-demo.vital-it.ch . Log in as user “test” with password “test”. You will be granted access to a variants database “demo”.
Try the following standard filters:
You should retreive a single variant on gene TBC1D7 that has been published in Hum Mutat. 2014 Apr;35(4):447-51.
Prior to making it public, this dataset has been anonymized and obfuscated. Parents variant data was generated by random shuffling variants from several independent exome datasets. Children variant data was derived from the shuffled parents data. The TBC1D7 pathogenic variant was then added following recessive pattern of inheritance.
This version runs on minimal hardware, thus its performance is not comparable to a real production setup.
If you liked it, we encourage you to deploy an instance at your own lab and share the experience.
App main developer: Julien Delafontaine