igv-screenshots

Generate publication-ready IGV screenshots from BAM files and region definitions.

Updated Jun 13, 2025

Search Tags:#screenshots #bioinformatics #visualization #genomics #bam #regions #igv

Ready to run

npx skills add https://github.com/sahuno/llm_configs --skill igv-screenshots

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: igv-screenshots
Source: https://github.com/sahuno/llm_configs/tree/main/claude/skills/igv-screenshots
Command: npx skills add https://github.com/sahuno/llm_configs --skill igv-screenshots

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

Generating consistent, publication-quality IGV screenshots from BAM files and region definitions can be tedious and error-prone; this skill automates the process to produce reliable visuals quickly.

Core Features & Use Cases

Automated IGV screenshot generation from one or more BAMs and a regions file.
Supports methylation coloring (ONT/PacBio), haplotype coloring, and multi-sample comparisons.
Use case: generate visuals for multiple regions across samples for publications or reports.

Quick Start

Run the IGV screenshot workflow by providing BAMs and a regions file; outputs are saved in an organized directory structured as IGV_{genome}_{description}.

Frequently Asked Questions about igv-screenshots

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

FAQPage Schema

How do I automate IGV screenshots from BAM files for multiple genomic regions?▼

You can automate IGV screenshots by providing indexed BAM files, a regions file (BED or text), and a genome specification. The workflow outputs publication-ready visuals organized in an IGV_{genome}_{description} directory.

Can I generate IGV screenshots for multi-sample comparisons across genomic regions?▼

Yes, the workflow supports multi-sample comparisons across genomic regions. You provide multiple BAM files with indices, and it generates comparative publication-quality IGV screenshots for the specified regions.

Does the IGV screenshot workflow support methylation and haplotype visualization?▼

Yes, the workflow supports methylation coloring for ONT and PacBio reads alongside haplotype visualization options. These features enable specialized tracking of epigenetic modifications and phased variants directly in the screenshots.

What do I need to run an automated IGV screenshot generation workflow?▼

You need indexed BAM files, a regions file (BED or text), a genome specification, and an IGV or igver container via Singularity or Docker. Optional configurations allow customizing colors and display settings for the output visuals.

What is the best way to create publication-quality IGV visuals from sequencing data?▼

Using an automated containerized workflow ensures consistent, publication-ready IGV visuals from BAM files and region definitions. This approach eliminates manual screenshot errors and standardizes output across multiple samples and genomic regions.