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IGVer

Conveniently take IGV snapshots of multiple BAM files over multiple genomic regions.

New in v0.2.0:

  • Updated to IGV version 2.19.5 (from 2.17.4)
  • Added support for BED format input files (BED3 and BED6)
  • Improved region file parsing
  • Added support for multiple output formats (PNG, SVG, PDF)

Container Versions:

  • sahuno/igver:latest - Always the most recent version (recommended)
  • sahuno/igver:2.19.5 - Specific version with IGV 2.19.5
  • Version tags available starting from 2.19.5

Table of Contents

Features

  • Generate high-resolution IGV screenshots programmatically
  • Support for multiple BAM files and multiple genomic regions
  • BED file support (BED3 and BED6 formats)
  • Run IGV in a containerized environment for reproducibility
  • Integrate with Python scripts using the API
  • Customize IGV display preferences

Requirements

  • Python 3.7+
  • Singularity/Apptainer or Docker
  • For local installation: matplotlib, Pillow, PyYAML

Installation

Option 1: Using Container (Recommended)

# For Docker
docker pull sahuno/igver:latest

# For Singularity/Apptainer
singularity pull docker://sahuno/igver:latest

Available versions:

  • sahuno/igver:latest - Always the most recent version (recommended)
  • sahuno/igver:2.19.5 - Specific version with IGV 2.19.5

Option 2: Local Installation

pip install igver

Note: Local installation still requires Singularity to run IGV.

Container Usage Important Notes

Docker: Works automatically - the container environment is auto-detected.

Singularity: You MUST use the --no-singularity flag to prevent nested container issues:

singularity exec docker://sahuno/igver:latest igver ... --no-singularity

This is because IGVer was originally designed to wrap IGV in a Singularity container, but when IGVer itself runs in a container, this creates a nested container problem.

Quick Start

# Using Docker
docker run --rm \
  -v $(pwd):/data \
  -v $(pwd)/output:/output \
  sahuno/igver:latest \
  igver -i /data/sample.bam -r "chr1:1000000-2000000" -o /output/

# Using Singularity (IMPORTANT: use --no-singularity flag)
singularity exec \
  -B $(pwd):/data \
  -B $(pwd)/output:/output \
  docker://sahuno/igver:latest \
  igver -i /data/sample.bam -r "chr1:1000000-2000000" -o /output/ --no-singularity

# Using local installation (requires Singularity)
igver -i sample.bam -r "chr1:1000000-2000000" -o output/

# Using BED file for regions
igver -i sample.bam -r regions.bed -o output/ --no-singularity

Important Note for Container Users: When running IGVer inside a container (Docker or Singularity), you must use the --no-singularity flag with Singularity to prevent nested container execution. Docker automatically detects the container environment.

Usage

CLI

Basic Usage

igver \
  -i test/test_tumor.bam test/test_normal.bam \
  -r "chr1:1000000-2000000" \
  -o ./screenshots

Using BED Files

# BED3 format (chr, start, end)
igver \
  -i sample.bam \
  -r regions.bed \
  -o ./screenshots

# BED6 format (includes region names in output)
igver \
  -i sample.bam \
  -r regions_with_names.bed \
  -o ./screenshots

Multiple Regions

# Multiple regions in one panel
igver \
  -i sample.bam \
  -r "chr1:1000-2000 chr2:3000-4000" \
  -o ./screenshots

# Multiple separate regions
igver \
  -i sample.bam \
  -r "chr1:1000-2000" "chr2:3000-4000" \
  -o ./screenshots

Command Line Options

igver --help

Options:
  -i, --input         Input BAM/BEDPE/VCF/bigWig file(s)
  -r, --regions       Genomic regions or BED file
  -o, --output        Output directory (default: /tmp)
  -g, --genome        Reference genome (default: hg19)
  --dpi               Output resolution (default: 300)
  -p, --max-panel-height   Maximum panel height (default: 200)
  -d, --overlap-display    Display mode: expand/collapse/squish (default: squish)
  -c, --igv-config    Custom IGV preferences file
  -f, --format        Output format: png/svg/pdf (default: png)
  --singularity-image Container image (default: docker://sahuno/igver:latest)
  --no-singularity    Run IGV directly without Singularity wrapper (required when using Singularity)
  --debug             Enable debug logging

Python API

Basic Example

import igver

# Generate screenshots
figures = igver.load_screenshots(
    paths=['tumor.bam', 'normal.bam'],
    regions=['chr1:1000000-2000000', 'chr2:3000000-4000000'],
    output_dir='./screenshots',
    genome='hg19'
)

# Save figures
for i, fig in enumerate(figures):
    fig.savefig(f'screenshot_{i}.png', dpi=300, bbox_inches='tight')

API Reference

igver.load_screenshots(
    paths,              # List of input files
    regions,            # List of regions or BED file
    output_dir='/tmp',  # Output directory
    genome='hg19',      # Reference genome
    igv_dir='/opt/IGV_2.19.5',
    overwrite=True,     # Overwrite existing files
    remove_png=True,    # Remove temporary PNGs
    dpi=300,            # Figure resolution
    singularity_image='docker://sahuno/igver:latest',
    **kwargs            # Additional IGV options
)

Supported File Formats

Input Files

  • BAM files (requires .bai index files)
  • BEDPE files (for structural variants)
  • VCF files (variant calls)
  • bigWig files (coverage tracks)

Region Files

  • BED3: chromosome<TAB>start<TAB>end
  • BED6: chromosome<TAB>start<TAB>end<TAB>name<TAB>score<TAB>strand
  • Text: Custom format with optional annotations

Output Formats

  • PNG (default): Raster format, best for publications
  • SVG: Vector format, scalable without quality loss
  • PDF: Converted from SVG, requires cairosvg (pip install igver[pdf])

Output File Naming

  • Single region: chr1-1000000-2000000.png
  • BED with name: chr1-1000000-2000000.gene_name.png
  • Multiple regions: chr1-1000-2000.chr2-3000-4000.png
  • With annotation: chr1-1000000-2000000.annotation.png

Examples

Example 1: Simple Screenshot

igver -i sample.bam -r "chr1:1000000-2000000" -o ./

Creates: ./chr1-1000000-2000000.png

Example 2: Structural Variant Visualization

# Create a regions file for a translocation
echo -e "chr8:128750000-128760000\tchr14:106330000-106340000\ttranslocation" > sv_regions.bed

igver \
  -i tumor.bam normal.bam \
  -r sv_regions.bed \
  -o ./sv_screenshots

Example 3: Different Output Formats

# Generate SVG (vector format)
igver -i sample.bam -r "chr1:1000000-2000000" -f svg -o ./

# Generate PDF (requires cairosvg)
pip install igver[pdf]  # Install PDF support
igver -i sample.bam -r "chr1:1000000-2000000" -f pdf -o ./

Example 4: Custom IGV Preferences

# Create custom preferences
cat > custom_prefs.txt << EOF
colorBy TAG HP
sort READNAME
group TAG RG
EOF

igver \
  -i sample.bam \
  -r regions.bed \
  -c custom_prefs.txt \
  -o ./screenshots

Advanced Usage

Working with Haplotagged Reads

# Create IGV preferences for haplotype visualization
cat > haplotype_view.batch << EOF
group TAG HP
colorBy TAG HP
sort READNAME
EOF

igver \
  -i haplotagged.bam \
  -r regions.bed \
  -c haplotype_view.batch \
  -p 500 \
  -o ./haplotype_screenshots

Batch Processing Multiple Samples

import igver
import glob

# Process all BAM files in a directory
bam_files = glob.glob("samples/*.bam")
regions = ["chr1:1000000-2000000", "chr2:3000000-4000000"]

for bam in bam_files:
    sample_name = os.path.basename(bam).replace('.bam', '')
    figures = igver.load_screenshots(
        paths=[bam],
        regions=regions,
        output_dir=f'screenshots/{sample_name}'
    )

Performance Tips

  • Pre-pull containers: Download container images before running to avoid delays
  • Use absolute paths: Provide absolute paths for files to avoid binding issues
  • Bind directories: Use -B or --bind flags to mount data directories
  • Memory allocation: Ensure sufficient memory for large genomic regions
  • Parallel processing: Process multiple samples in parallel when possible

Troubleshooting

Container Issues

  • "singularity: command not found" error when using Singularity: You must use the --no-singularity flag:

    singularity exec docker://sahuno/igver:latest igver ... --no-singularity

    This prevents IGVer from trying to run Singularity inside the container.

  • Permission denied: Add bind flags for your data directories

    singularity exec -B /data,/home docker://sahuno/igver:latest igver ... --no-singularity

  • Image not found: Pull the image first

    singularity pull docker://sahuno/igver:latest

Common Errors

  • No screenshots generated:

    • Check if BAM files have indexes (.bai files)
    • Verify chromosome names match reference genome (chr1 vs 1)
    • Check output directory permissions

  • Region not found:

    • Verify chromosome naming convention
    • Check if regions are within chromosome bounds
    • Ensure genome version matches your data

IGV Display Issues

  • Screenshot width: Modify IGV preferences file 
    # In container: /opt/IGV_2.19.5/prefs.properties
# Set: IGV.Bounds=0,0,800,480 for 800px width

License

MIT License - see LICENSE file for details

Authors

  • Seongmin Choi (@soymintc) - Original author
  • Contributors welcome!

Citation

If you use IGVer in your research, please cite:

Choi, S. (2024). IGVer: Automated IGV Screenshot Generation for Genomics. 
GitHub: https://github.com/shahcompbio/igver

Contributing

Contributions are welcome! Please feel free to submit a Pull Request.

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Automatically take IGV snapshots

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automation bioinformatics igv bioinformatics-tool

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