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VariantGrid is a database and web application for storing, analysing and classifying variants.
Upload VCFs to:
- See all samples that share a variant
- Analyse and filter samples, including real time drag & drop interactive analyses
- Classify variants using customisable ACMG form
- Manage and curate data, including patient phenotypes
Research use is free, while commercial use requires a licence, before code becomes fully free/open source in 4 years. This is our attempt to obtain sustainable funding to for future development. See Licence discussion
VariantGrid has been used for private servers:
- VariantGrid is in clinical/diagnostic use by SA Pathology, the South Australian public pathology service.
- Research server used by labs at the Centre for Cancer Biology
The technology is also used on public data sharing sites:
- https://shariant.org.au - Australian Genomics variant classification sharing server
- https://runx1db.runx1-fpd.org - Rare blood disease data sharing
This wiki is for a technical audience looking to install/modify VariantGrid code. For users of the software, please see:
User guide at read the docs VariantGrid.com main site, and research cloud server
- Installation
- Technical Overview
- VCF and data
- Annotation
- Genes and Variants
- Analysis
- Classification
- Development
- Contact us and we can setup and manage a cloud instance for you
- Install from source
- Clone a VM (AWS, VirtualBox, NECTAR, NCBI instances)
VariantGrid is written in Python3 using Django and PostgreSQL.
The project aims at integrating with existing mapping & variant calling pipelines and patient record systems
10-100k samples, mostly exomes Multi-sample analysis is done on samples from same VCF Run on a reasonably beefy server (4-16 cores, 10G RAM, SSD preferred) Optimise for bioinformatician productivity vs raw performance
- Samples are stored in
10-100k