bedtools/bedtools_igv

genomics

visualization

igv

screenshots

batch

automation

intervals

Description

Create IGV batch script to generate automated screenshots of genomic regions.

This tool generates a batch script that can be run within IGV (Integrative Genomics Viewer)
to automatically create image snapshots at each interval defined in a BED/GFF/VCF file.
Useful for creating automated visualizations of genomic features or regions of interest.

Type

bash_script

License

MIT

Keywords

genomics

visualization

igv

screenshots

batch

automation

intervals

Links

Repository

Documentation

Contributors

Launch

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
output: "$id.$key.output.txt"  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/biobox.git \  
  -revision v0.4.0 \  
  -main-script target/nextflow/bedtools/bedtools_igv/main.nf \  
  -params-file params.yaml

Inputs

Name	Type & Properties	Description
--input -i	file required	Input file with genomic intervals for visualization. Format: BED, GFF, or VCF file with genomic regions Usage: Each interval will generate one IGV screenshot Column 4: Optional name field used for image filenames (with --use_name)

Name

Type & Properties

--input

-i

file

required

Outputs

Name	Type & Properties	Description
--output	file required output	Output IGV batch script file. Format: Plain text script with IGV commands Usage: Run this script within IGV to generate automated screenshots Extension: Typically .txt or .igv

Name

Type & Properties

--output

file

required

output

Output Configuration

Name	Type & Properties	Description
--output_path --path	string	Full path where IGV snapshots should be written. Format: Directory path (must exist before running script) Default: Current directory (./) Example: "/path/to/igv/images/" Note: Include trailing slash for directories
--image_format --img	string	Image format for generated screenshots. Options: png, eps, svg Default: png Recommendation: PNG for most use cases

Name

Type & Properties

--output_path

--path

string

--image_format

--img

string

IGV Session Options

Name	Type & Properties	Description
--session_file --sess	file	Path to existing IGV session file to load before taking snapshots. Format: IGV session file (.xml) Purpose: Pre-loads genome, tracks, and display settings Optional: If not provided, assumes genome and tracks are already loaded

Name

Type & Properties

--session_file

--sess

file

Display Options

Name	Type & Properties	Description
--sort_reads --sort	string	BAM read sorting method to apply for each image. Options: base, position, strand, quality, sample, readGroup Default: No sorting applied Usage: Only relevant when BAM tracks are loaded in IGV
--collapse_reads --clps	boolean_true	Collapse aligned reads before taking snapshots. Effect: Shows read coverage instead of individual reads Usage: Useful for high-coverage regions Default: false (show individual reads)
--flank_size --slop	integer	Number of flanking base pairs on left and right of each region. Range: 0 or positive integer Default: 0 (no flanking) Purpose: Include context around regions of interest Example: 1000 adds 1kb padding on each side
--use_name --name	boolean_true	Use the name field (column 4) from input file for image filenames. Effect: Images named using BED name field instead of coordinates Default: false (use "chr:start-end.ext" format) Requirement: Input file must have name field (column 4)

Name

Type & Properties

--sort_reads

--sort

string

--collapse_reads

--clps

boolean_true

--flank_size

--slop

integer

--use_name

--name

boolean_true