How does it handle large-scale region lists?

The skill uses BED files for efficient batch processing, which allows IGV to process many regions in a single session rather than restarting for every region.

What is the primary use of this skill?

It automates the creation of genomic visualization snapshots using IGV, specifically designed for analyzing BAM alignment files and BED-defined regions.

Can I visualize multiple BAM files at once?

Yes, the skill supports loading multiple BAM files simultaneously, allowing you to compare alignments across different samples in a single snapshot.

Does it support different genome assemblies?

Yes, you can specify various genome assembly IDs such as hg38, hg19, or mm39, provided they are supported by your IGV installation.

Do I need to have IGV installed locally?

Yes, this skill requires a local installation of the Integrative Genomics Viewer (IGV) as it interacts with the software via its batch command interface.

IGV Integration

Name: IGV Integration
Author: dakesan

bydakesan

Data Science & ML

Automates IGV snapshot generation for visualizing genomic alignments and variant calls in BAM files.

About

The IGV Integration skill streamlines genomic data visualization by automating the generation of high-quality PNG screenshots through the Integrative Genomics Viewer (IGV). It enables bioinformaticians and researchers to batch-process multiple genomic regions defined in BED files, overlay multiple BAM tracks for comparative analysis, and manage IGV's batch command interface directly through Claude. This tool is specifically designed to accelerate WGS/WES quality control and variant validation workflows by replacing manual GUI interactions with reproducible automated scripts.

Key Features

Automated PNG snapshot generation for specific genomic loci
0 GitHub stars
Reproducible batch script generation for debugging and workflow documentation
Batch processing of multiple regions via BED file integration
Simultaneous multi-track BAM visualization for sample comparison
Customizable IGV parameters including panel height and Java heap size

Use Cases

Generating batch snapshots for high-throughput genomic quality control
Visualizing and validating variant calls across multiple patient samples
Inspecting BLAT alignment results and structural variant hit regions

About

Key Features

Automated PNG snapshot generation for specific genomic loci
0 GitHub stars
Reproducible batch script generation for debugging and workflow documentation
Batch processing of multiple regions via BED file integration
Simultaneous multi-track BAM visualization for sample comparison
Customizable IGV parameters including panel height and Java heap size

Use Cases

Generating batch snapshots for high-throughput genomic quality control
Visualizing and validating variant calls across multiple patient samples
Inspecting BLAT alignment results and structural variant hit regions