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igv-reports: embedding interactive genomic visualizations in HTML reports to aid variant review.

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Related Experiment Video

Updated: Jan 10, 2026

Visualizing Genetic Variants, Short Targets, and Point Mutations in the Morphological Tissue Context with an RNA In Situ Hybridization Assay
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igv-reports: Embedding interactive genomic visualizations in HTML reports to aid variant review.

James T Robinson1, Helga Thorvaldsdottir2, Jill P Mesirov1,3

  • 1Department of Medicine, School of Medicine, University of California San Diego, La Jolla, CA, USA.

Biorxiv : the Preprint Server for Biology
|November 24, 2025
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Summary

igv-reports is a command-line tool that generates standalone HTML pages for interactive genomic data visualization. These reports embed read alignments and annotations, simplifying variant inspection without external file dependencies.

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Last Updated: Jan 10, 2026

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Determining the Likelihood of Variant Pathogenicity Using Amino Acid-level Signal-to-Noise Analysis of Genetic Variation
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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Variant inspection is crucial for genomic analysis.
  • Existing tools may require complex setups or external data.
  • Streamlining visualization workflows is essential for efficient research.

Purpose of the Study:

  • To introduce igv-reports, a novel command-line tool.
  • To enable the creation of self-contained HTML reports with interactive genomic visualizations.
  • To facilitate variant inspection by embedding all necessary data and code.

Main Methods:

  • Developed a command-line tool named igv-reports.
  • Implemented functionality to generate standalone HTML pages.
  • Integrated interactive visualization of read alignments and annotations.

Main Results:

  • igv-reports successfully creates self-contained HTML reports.
  • These reports embed interactive genomic visualizations.
  • The generated reports require no external data file dependencies for visualization.

Conclusions:

  • igv-reports simplifies the process of sharing and inspecting genomic variant data.
  • The tool enhances variant inspection workflows by providing accessible, interactive reports.
  • Standalone HTML reports improve data reproducibility and ease of use in genomics research.