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igv-reports

Generate interactive HTML genomic region reports from BAM/VCF data.

Updated May 18, 2026
Search Tags:#report generation#genomics#cohort analysis#igv#igv-reports
One-click install
npx skills add https://github.com/sahuno/igv-reports-skill --skill igv-reports
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: igv-reports
Source: https://github.com/sahuno/igv-reports-skill/tree/main
Command: npx skills add https://github.com/sahuno/igv-reports-skill --skill igv-reports

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires igv-reports>=1.16.0, samtools, and includes scripts (resource) and references (resource) components.

What problem does it solve?

This Skill simplifies the process of generating interactive HTML reports for genomic data, allowing users to view and analyze genomic regions offline.

Core Features & Use Cases

  • Build Reports: Create self-contained HTML reports for genomic regions using BAM/VCF data, default annotation tracks, and custom tracks.
  • Cohort Analysis: Generate reports for multiple samples in a cohort with a single command.
  • Content Verification: Perform structural and content verification on generated reports to ensure data accuracy.
  • Use Case: If you have a set of genomic samples with BAM/VCF data and want to generate interactive reports for each sample, this Skill can automate the process.

Quick Start

To generate an HTML report for a single sample, use the command:

python scripts/build_igvreports.py --genome hg38 --sites sites.hg38.bed --bam tumor.bam normal.bam --output report.hg38.html

Frequently Asked Questions about igv-reports

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I generate interactive HTML reports for genomic data?▼

Generate interactive genomic reports by processing BAM and VCF files with annotation tracks into self-contained HTML documents, enabling offline visualization and collaborative analysis of genomic regions.

Can I create cohort analysis reports for multiple genomic samples at once?▼

Cohort analysis reports can be generated for multiple genomic samples simultaneously, automating the creation of interactive HTML reports for each sample using a single command to streamline downstream collaborative analysis.

What is the best way to view and analyze genomic regions offline?▼

Building self-contained HTML reports from BAM or VCF data provides the best way to view and analyze genomic regions offline, embedding interactive visualization and default annotation tracks directly within the output file.

Do I need samtools to verify the content of generated genomic reports?▼

Samtools is optionally required to perform structural and content verification on generated genomic reports, ensuring data accuracy within the output HTML files, while igv-reports version 1.16.0 or higher is strictly required.

Does igv-reports support custom annotation tracks for genomic visualization?▼

Custom annotation tracks are supported alongside default tracks for genomic visualization, allowing users to incorporate specific reference data into the interactive HTML reports generated from BAM and VCF input files.

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