Bioinformatics Made Accessible

Whole Exome Sequencing
Analysis Made Simple

Var|Decrypt is a user-friendly web-based tool designed to empower clinicians and biologists to analyze WES data without requiring extensive bioinformatics expertise. Extract meaningful insights from your genomic data in minutes, not months.

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Capabilities

Powerful Features for WES Analysis

Comprehensive tools to filter, cluster, and enrich your variant data with intuitive interfaces

Advanced Filtering

Filter variants by gene, position, quality scores, population frequency, and functional impact. Customizable filters help you focus on the most relevant variants for your research.

Clustering Analysis

Identify patterns and relationships in your variant data through sophisticated clustering algorithms. Visualize complex genomic relationships with interactive plots.

Enrichment Tools

Perform pathway enrichment and gene ontology analysis to understand the biological significance of your variants. Discover functional themes in your data.

Variant Prioritization

Intelligently rank variants based on pathogenicity predictions, clinical databases, and functional annotations to identify the most promising candidates.

User-Friendly Interface

No command-line required. Intuitive RShiny interface designed specifically for biologists and clinicians without extensive bioinformatics training.

Patient-Specific Insights

Extract personalized functional information from patient datasets. Compare across samples and identify disease-specific patterns and potential therapeutic targets.

Applications

Validated Across Multiple Diseases

Proven effectiveness in cancer genomics and beyond

Acute Erythroid Leukemia

Successfully identified known oncogenes and novel putative drivers in 10 AEL patients, demonstrating utility in rare and aggressive cancers.

Multiple Myeloma

Validated on ~90 WES samples, recapitulating known deregulated genes and pathways, confirming robustness across different cancer types.

Cancer Genomics

Discover driver mutations, tumor suppressor genes, and therapeutic targets in various cancer types through comprehensive variant analysis.

Clinical Diagnostics

Accelerate diagnostic workflows by rapidly identifying causative variants in patients with genetic disorders or unexplained phenotypes.

Proven Results

Rigorous Validation on Real Clinical Data

Var|Decrypt has been extensively validated on multiple independent datasets, demonstrating its ability to accurately identify disease drivers and deregulated pathways.

Our validation studies successfully recovered known oncogenes in acute erythroid leukemia patients and identified novel putative drivers, showcasing the tool's discovery potential.

  • Validated on 10 acute erythroid leukemia WES datasets
  • Confirmed with ~90 multiple myeloma samples
  • Successfully identified known disease oncogenes
  • Discovered novel putative driver mutations
  • Recapitulated established deregulated pathways
Getting Started

Installation via Docker

Run Var|Decrypt locally on your machine using Docker - no complex setup required

Prerequisites

  • Docker installed on your system (Get Docker)
  • At least 4GB of available RAM
  • Internet connection for initial download

Pre-Var|Decrypt - Data Preparation

Streamlined interface for VCF file preparation and initial quality control. Start here to prepare your data before main analysis.

For AMD64 / Intel processors

Pull the Docker image: 
docker pull mohammadsalma/pre_vardecrypt_amd64
Run the container: 
docker run --cpus=0.000 --mount type=bind,source=/path_to_YourData/,target=/root/WorkingDir -it -p 3837:3837 -t mohammadsalma/pre_vardecrypt_amd64

For ARM processors (Mac M1/M2/M3 or later)

Pull the Docker image: 
docker pull mohammadsalma/pre_vardecrypt_arm
Run the container: 
docker run --cpus=0.000 --mount type=bind,source=/path_to_YourData/,target=/root/WorkingDir -it -p 3837:3837 -t mohammadsalma/pre_vardecrypt_arm
Access at: http://0.0.0.0:3837

Var|Decrypt - Main Application

Full-featured variant analysis and prioritization interface for comprehensive WES data exploration.

For AMD64 / Intel processors

Run the container: 
docker run --cpus=0.000 -it -p 3838:3838 -t mohammadsalma/vardecryptamd64

For ARM processors (Mac M1/M2/M3 or later)

Run the container: 
docker run --cpus=0.000 -it -p 3838:3838 -t mohammadsalma/vardecryptarm
Access at: http://0.0.0.0:3838

Running Both Applications

You can run both containers simultaneously on different ports (3838 for Var|Decrypt, 3839 for Pre-Var|Decrypt). Use Pre-Var|Decrypt first to prepare your data, then analyze with Var|Decrypt.

Stopping Containers

To stop a running container, use: docker stop $(docker ps -q --filter ancestor=mohammadsalma/vardecrypt)

More Information

For advanced usage, troubleshooting, and source code, visit our GitLab repository.

Learn

Video Tutorials

Watch step-by-step guides to get started with Var|Decrypt and Pre-Var|Decrypt

Pre-Var|Decrypt Tutorial

Learn how to prepare and preprocess your VCF files using the Pre-Var|Decrypt interface. Start here for data preparation.

Var|Decrypt Tutorial

Comprehensive guide to using the main Var|Decrypt application for variant analysis and prioritization.

Publication

How to Cite

If you use Var|Decrypt in your research, please cite our publication

Salma, M., Alaterre, E., Moreaux, J. et al. Var∣Decrypt: a novel and user-friendly tool to explore and prioritize variants in whole-exome sequencing data. Epigenetics & Chromatin 16, 23 (2023).

https://doi.org/10.1186/s13072-023-00497-4

Received

13 January 2023

Accepted

23 May 2023

Published

14 June 2023

Version of Record

14 June 2023

BibTeX Format

BibTeX citation: 
@article{Salma2023,
  author = {Salma, Mohammad and Alaterre, Elina and Moreaux, Jérôme and others},
  title = {Var∣Decrypt: a novel and user-friendly tool to explore and prioritize variants in whole-exome sequencing data},
  journal = {Epigenetics \& Chromatin},
  year = {2023},
  volume = {16},
  number = {23},
  doi = {10.1186/s13072-023-00497-4},
  url = {https://doi.org/10.1186/s13072-023-00497-4}
}

Ready to Unlock Your WES Data?

Join researchers and clinicians worldwide using Var|Decrypt to accelerate their genomic discoveries. Get started with Docker in minutes.

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Resources

Get Started with Var|Decrypt

Everything you need to begin analyzing your WES data

User Tutorial

Comprehensive step-by-step guide covering all features and functionalities. Perfect for first-time users and advanced workflows.

Read Tutorial

Source Code

Full source code available on GitLab. Customize, extend, or deploy Var|Decrypt on your own infrastructure.

View Repository

Research Publication

Read our peer-reviewed publication detailing the development, validation, and applications of Var|Decrypt.

View Citation