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.
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) |
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 |
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 |
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 |
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) |
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 Relationships
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Current component
bedtools/bedtools_igvbiobox v0.4.0
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