Variant annotation with SnpEff tutorial

Allie Cliffe
  • Updated

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.

Terra-on-Azure_snpeff1.png

Visual.2: Highlight of SnpEff variant annotation summary report 

Terra-on-Azure_snpeff2.png

Visual.3: Convert SnpEff output to pandas table. 

Terra-on-Azure_snpeff3.png

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

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