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bio-igv This skill should be used when the user needs to visualize BAM alignment files in IGV (Integrative Genomics Viewer). Triggers include requests to generate IGV screenshots, visualize genomic regions with multiple BAM tracks, or create batch visualizations for WGS analysis results.
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name bio-igv description This skill should be used when the user needs to visualize BAM alignment files in IGV (Integrative Genomics Viewer). Triggers include requests to generate IGV screenshots, visualize genomic regions with multiple BAM tracks, or create batch visualizations for WGS analysis results. user_invocable true
IGV Integration
Automated IGV (Integrative Genomics Viewer) snapshot generation for genomic regions with multiple BAM files. Designed for WGS/WES analysis visualization and quality control.
Quick Start
Install
Install IGV:
brew install --cask igv
wget https://data.broadinstitute.org/igv/projects/downloads/2.16/IGV_Linux_2.16.0_withJava.zip
unzip IGV_Linux_2.16.0_withJava.zip
Install Python dependencies:
uv pip install typer
Basic Usage
python scripts/generate_igv_snapshots.py \
--genome hg38 \
--bam sample1.bam sample2.bam sample3.bam \
--region chr1:1000-2000 \
--output-dir ./igv_snapshots
python scripts/generate_igv_snapshots.py \
--genome hg38 \
--bam sample1.bam sample2.bam \
--bed regions.bed \
--output-dir ./igv_snapshots
Scripts
generate_igv_snapshots.py - IGV Snapshot Generation
Generate PNG screenshots of genomic regions with multiple BAM tracks using IGV batch mode.
Required Arguments
--genome TEXT - Genome assembly ID (e.g., hg38, hg19, mm39)--bam PATH - BAM file path(s). Can specify multiple files.--region TEXT or --bed PATH - Either single region (e.g., chr1:1000-2000) or BED file with multiple regions--output-dir PATH - Output directory for snapshots
Optional Arguments
--igv-path TEXT - Path to IGV executable (default: auto-detect)--max-panel-height INT - Maximum panel height in pixels (default: 500)--java-heap TEXT - Java heap size (default: 2g)
--save-batch-script - Save IGV batch script for debugging (default: False)
Output Format
Named by region: chr1_1000-2000.png
Or by BED name field: region_name.png
Optional Batch Script (with --save-batch-script):
igv_batch_script.txt - IGV commands used for snapshot generation
Usage Examples
python scripts/generate_igv_snapshots.py \
--genome hg38 \
--bam control.bam treatment1.bam treatment2.bam \
--region chr1:1000-2000 \
--output-dir ./snapshots
python scripts/generate_igv_snapshots.py \
--genome hg38 \
--bam alignment.bam \
--bed regions_of_interest.bed \
--output-dir ./snapshots
python scripts/generate_igv_snapshots.py \
--genome hg38 \
--bam sample.bam \
--region chr1:1000-2000 \
--output-dir ./snapshots \
--max-panel-height 800 \
--java-heap 4g
python scripts/generate_igv_snapshots.py \
--genome hg38 \
--bam sample.bam \
--region chr1:1000-2000 \
--output-dir ./snapshots \
--save-batch-script
Workflow Examples
Example 1: Visualize BLAT Results Visualize BLAT alignment results from BAM file:
echo -e "chr1\t1000\t2000\tinsert1" > blat_hits.bed
echo -e "chr2\t5000\t6000\tinsert2" >> blat_hits.bed
python scripts/generate_igv_snapshots.py \
--genome hg38 \
--bam alignment.bam \
--bed blat_hits.bed \
--output-dir ./blat_visualizations
Example 2: Compare Multiple Samples Visualize the same regions across multiple BAM files:
python scripts/generate_igv_snapshots.py \
--genome hg38 \
--bam sample1.bam sample2.bam sample3.bam \
--bed candidate_regions.bed \
--output-dir ./multi_sample_comparison
Example 3: Validate Variant Calls Visualize variant sites with BAM alignment:
bcftools query -f '%CHROM\t%POS0\t%END\t%ID\n' variants.vcf > variant_sites.bed
python scripts/generate_igv_snapshots.py \
--genome hg38 \
--bam alignment.bam \
--bed variant_sites.bed \
--output-dir ./variant_validation \
--max-panel-height 600
IGV Batch Script Format The script generates IGV batch commands in this format:
new
genome hg38
load /path/to/sample1.bam
load /path/to/sample2.bam
snapshotDirectory /path/to/output
maxPanelHeight 500
goto chr1:1000-2000
snapshot chr1_1000-2000.png
goto chr2:5000-6000
snapshot chr2_5000-6000.png
exit
Error Handling
IGV Not Found $ python scripts/generate_igv_snapshots.py --genome hg38 --bam sample.bam --region chr1:1000-2000 --output-dir ./out
Error: IGV not found. Please install IGV or specify path with --igv-path.
Install: brew install --cask igv (macOS) or download from https://software.broadinstitute.org/software/igv/download
Solution: Install IGV or specify path:
brew install --cask igv
python scripts/generate_igv_snapshots.py \
--genome hg38 \
--bam sample.bam \
--region chr1:1000-2000 \
--output-dir ./out \
--igv-path /path/to/igv.sh
Invalid Region Format $ python scripts/generate_igv_snapshots.py --genome hg38 --bam sample.bam --region 1000-2000 --output-dir ./out
Error: Invalid region format: 1000-2000. Expected format: chr1:1000-2000
Solution: Use correct region format chr:start-end:
python scripts/generate_igv_snapshots.py \
--genome hg38 \
--bam sample.bam \
--region chr1:1000-2000 \
--output-dir ./out
No Snapshots Generated $ python scripts/generate_igv_snapshots.py --genome hg38 --bam sample.bam --region chr1:1000-2000 --output-dir ./out
Snapshots generated successfully in : ./out
Total regions processed: 1
Warning: No snapshots found. Check IGV output for errors.
BAM file not indexed (create with samtools index)
Region not present in BAM file
IGV failed to start (check --save-batch-script for debugging)
samtools index sample.bam
python scripts/generate_igv_snapshots.py \
--genome hg38 \
--bam sample.bam \
--region chr1:1000-2000 \
--output-dir ./out \
--save-batch-script
igv.sh -b ./out/igv_batch_script.txt
Best Practices
1. Always Index BAM Files Create BAM index before generating snapshots:
samtools index sample1.bam
samtools index sample2.bam
python scripts/generate_igv_snapshots.py \
--genome hg38 \
--bam sample1.bam sample2.bam \
--region chr1:1000-2000 \
--output-dir ./snapshots
2. Use BED Files for Multiple Regions For batch processing, use BED files instead of multiple script calls:
python scripts/generate_igv_snapshots.py \
--genome hg38 \
--bam sample.bam \
--bed regions.bed \
--output-dir ./snapshots
python scripts/generate_igv_snapshots.py --bam sample.bam --region chr1:1000-2000 --output-dir ./out
python scripts/generate_igv_snapshots.py --bam sample.bam --region chr2:5000-6000 --output-dir ./out
3. Adjust Panel Height for Readability Increase panel height when visualizing multiple BAM tracks:
python scripts/generate_igv_snapshots.py \
--genome hg38 \
--bam s1.bam s2.bam s3.bam s4.bam s5.bam \
--region chr1:1000-2000 \
--output-dir ./snapshots \
--max-panel-height 800
4. Use Appropriate Genome Assembly Match genome assembly to BAM file reference:
samtools view -H alignment.bam | grep @SQ
python scripts/generate_igv_snapshots.py \
--genome hg38 \
--bam alignment.bam \
--region chr1:1000-2000 \
--output-dir ./snapshots
When to Use igv-integration vs Manual IGV Task igv-integration Manual IGV Visualize many regions (>10) ✅ generate_igv_snapshots.py ❌ Too tedious Generate publication figures ✅ Reproducible batch mode ✅ Fine-tuned manual control Compare multiple samples ✅ Load all BAMs at once ✅ Interactive comparison Validate variant calls ✅ Automate with BED file ✅ Interactive inspection Explore data interactively ❌ Use manual IGV ✅ Full GUI control
Use igv-integration for batch snapshot generation
Use manual IGV for interactive exploration and fine-tuning
Combine both for comprehensive analysis
Related Skills
bam-toolkit - BAM file analysis and read extractionvcf-toolkit - VCF variant analysisblat-api-searching - BLAT genome mapping to find regions for visualizationsequence-io - FASTA/FASTQ sequence operations
Troubleshooting
Java Heap Size Errors If IGV fails with memory errors, increase Java heap size:
python scripts/generate_igv_snapshots.py \
--genome hg38 \
--bam large_file.bam \
--region chr1:1000-2000 \
--output-dir ./out \
--java-heap 4g
Chromosome Name Mismatch Ensure chromosome names match between BAM file and region specification:
samtools idxstats sample.bam | cut -f1
python scripts/generate_igv_snapshots.py \
--genome hg38 \
--bam sample.bam \
--region 1:1000-2000 \
--output-dir ./out
BED File Format Errors Ensure BED file has at least 3 columns (chrom, start, end):
chr1 1000 2000
chr2 5000 6000 region_name
chr1:1000-2000
References 