Whole-exome sequencing · RShiny

Explore and prioritise
exome variants.

Move from variant tables to genes and pathways. Explore somatic and germline variants, compare samples and investigate functional enrichment through an interactive interface.

Install with Docker Watch the tutorials

Developed by Mohammad Salma at IGMM, Montpellier.

Inside Var|Decrypt
Var|Decrypt General statistics tab: variant classification, variant types, SNV classes, variants per sample and the top 20 mutated genes.
General statistics — examine variant classes, compare samples and inspect recurrently mutated genes. From the Var|Decrypt documentation. Select the image to view it full size.
Published in Epigenetics & Chromatin, 2023Read the paper

The tool

Keep the biological
question in view.

Browse individual genes or look across a cohort. Var|Decrypt brings variant exploration and downstream analyses into the same workspace.

Explore genes
and variants

Browse somatic or germline data, select mutation types and inspect the samples carrying variants in a gene. Sort gene lists by mutation frequency.

Compare samples
and patterns

Use variant summaries, oncoplots and clustering to examine differences across samples. Inspect variant counts to spot outliers before further analysis.

Investigate genes
in context

Explore pathway and disease enrichment, oncogenic signalling pathways and gene associations to select candidates for functional follow-up.

Explore the illustrated user guide

The workflow

Two applications.
One analysis workflow.

Start with VCF files from your variant-calling pipeline. Pre-Var|Decrypt prepares the inputs; Var|Decrypt provides the exploration interface.

  1. Prepare your VCF files

    Use Pre-Var|Decrypt to generate the input files required by the main application.

    Pre-Var|Decrypt · port 3837

  2. Explore the resulting data

    Load the prepared files into Var|Decrypt, choose somatic or germline analysis, then filter and compare.

    Var|Decrypt · port 3838

  3. Return to your analysis

    Save processed results as an RData file and reload them in a later session.

Research

Evaluated on
published WES datasets.

The 2023 study applied Var|Decrypt to two cancer datasets to explore mutated genes and associated biological pathways.

10 patients

Acute erythroid leukaemia

The analysis recovered known oncogenes and highlighted additional putative drivers for investigation.

~90 exomes

Multiple myeloma

An independent dataset reproduced previously reported deregulated genes and pathways.

These are research case studies. See the paper for datasets, methods and the scope of the evaluation.

Read the methods and results

Installation

Run it on your machine.

Install Docker and start it before running the commands below. Choose the images for your processor. The first run downloads the images and requires an internet connection.

Replace /absolute/path/to/your/data with the full path to your data folder. Keep the quotation marks if the path contains spaces. Run each application in its own terminal.

Intel / AMD · x86-64

1. Prepare your data

Pre-Var|Decrypt

Terminal
docker run -it \
  -p 127.0.0.1:3837:3837 \
  --mount "type=bind,source=/absolute/path/to/your/data,target=/root/WorkingDir" \
  mohammadsalma/pre_vardecrypt_amd64

2. Explore the prepared files

Var|Decrypt

Terminal
docker run -it \
  -p 127.0.0.1:3838:3838 \
  mohammadsalma/vardecryptamd64
Apple Silicon / ARM64

1. Prepare your data

Pre-Var|Decrypt

Terminal
docker run -it \
  -p 127.0.0.1:3837:3837 \
  --mount "type=bind,source=/absolute/path/to/your/data,target=/root/WorkingDir" \
  mohammadsalma/pre_vardecrypt_arm

2. Explore the prepared files

Var|Decrypt

Terminal
docker run -it \
  -p 127.0.0.1:3838:3838 \
  mohammadsalma/vardecryptarm

Open in your browser: localhost:3837 for preparation and localhost:3838 for analysis. Both applications can run at the same time.

Stop an application: press Ctrl + C in its terminal. For configuration and troubleshooting, see the repository documentation.

Tutorials

Follow the analysis, step by step.

Start with data preparation, then continue in the main application.

02 / Variant exploration

Var|Decrypt

Load your data and explore the analysis interface.

Watch on YouTube

Publication

Cite Var|Decrypt.

If you use the tool in your research, please cite the original paper.

Salma, M., Alaterre, E., Moreaux, J. & Soler, E. 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

Read the publication
BibTeX citation
@article{Salma2023,
  author = {Salma, Mohammad and Alaterre, Elina and Moreaux, Jérôme and Soler, Eric},
  title = {Var{\textbar}Decrypt: a novel and user-friendly tool to explore and prioritize variants in whole-exome sequencing data},
  journal = {Epigenetics \& Chromatin},
  year = {2023},
  volume = {16},
  pages = {23},
  doi = {10.1186/s13072-023-00497-4}
}