Variant annotation with SnpEff tutorial

Learn to use SnpEff in a notebook in Terra on Azure. 

Versatile variant Annotation with SnpEff

SnpEff is a flexible tool for annotating and predicting the effects of genetic variants. The SnpEff workspace provides genomics researchers a powerful platform for variant analysis and annotation [5]. 

Unique features that can be useful for reliable genomics annotation analysis

• Annotation support for the human genome, as well as all model organisms
• Can annotate up to 1,000,000 variants per minute
• Can be easily integrated with GATK and Galaxy pipelines

For a full list of features, see the SnpEff web page.

Try snpEff in Terra on Azure (tutorial workspace

You’ll find step-by-step instructions for using SnpEff in the tutorial workspace Variant Annotation with SnpEff - Dashboard (terra.bio). See sample outputs from the Jupyter notebook in the workspace below. 

Visual.1: Sample command and output of SnpEff variant annotation.

Visual.2: Highlight of SnpEff variant annotation summary report 

Visual.3: Convert SnpEff output to pandas table. 

References

1. Shiny for R: https://shiny.posit.co/r/getstarted/shiny-basics/lesson1/index.html
2. Shiny for R examples (GitHub): https://github.com/rstudio/shiny-examples
3. VS Code Server: https://code.visualstudio.com/docs/remote/vscode-server#_getting-started
4. VS Code : https://code.visualstudio.com/
5. Running SnpEff: https://pcingola.github.io/SnpEff/snpeff/running/
6. SnpEff at Microsoft Genomics Data Lake: https://learn.microsoft.com/en-us/azure/open-datasets/dataset-snpeff
7. Introduction - SnpEff & SnpSift (pcingola.github.io
8. Home - Galaxy Community Hub (galaxyproject.org