IGV Snapshot Automation

Automates IGV (Integrative Genomics Viewer) batch snapshot generation for multiple BAM files and genomic regions. Developed at CSIR-IGIB for rare disease WES variant visualization.

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What it does

• Reads BAM filenames and genomic regions from a text file
• Generates individual IGV batch scripts (.igv) for each sample
• Runs IGV in batch mode to capture PNG snapshots automatically

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Workflow

Step 1 — Prepare input file

Create bam_region.txt (tab or space separated):

SAMPLE001.bam chr1:99861524-99861524
SAMPLE002.bam chr2:218812300-218812300
SAMPLE003.bam chr3:38613773-38613773
SAMPLE004.bam chr3:165830741-165830741

Step 2 — Generate IGV scripts

python generate_igv_script.py \
  -b /path/to/BAMs \
  -s /path/to/snapshots \
  -g /path/to/hg38.fa \
  -r bam_region.txt

Step 3 — Run IGV batch

./run_igv.sh

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Arguments

Argument	Description
-b	Path to BAM files directory
-s	Directory to save PNG snapshots
-g	Path to genome reference (hg38)
-r	Path to BAM regions file
-d	Delay in seconds between samples (default: 2)

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Output

• .igv batch scripts per sample
• .png snapshots saved to snapshot directory

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Requirements

• Linux operating system
• Python 3.8+
• IGV installed and igv.sh in PATH

Tools Used

• IGV (Integrative Genomics Viewer)
• Python 3
• Bash

Author

Treesa Issen | CSIR-IGIB, New Delhi