bedtools/bedtools_cluster
genomics
intervals
clustering
overlap
proximity
grouping
Description
Cluster overlapping or nearby genomic intervals.
This tool groups genomic intervals into clusters based on overlap
or proximity within a specified distance. Each cluster is assigned
a unique cluster ID, making it useful for analyzing genomic feature
distributions and relationships.
Inputs
Name | Type & Properties | Description |
|---|---|---|
--input -i | file required | Input file in BED, GFF, or VCF format. **BED format:** Standard genomic interval format **GFF format:** Gene feature format with annotations **VCF format:** Variant call format **Requirements:** Must be sorted by chromosome and position |
Outputs
Name | Type & Properties | Description |
|---|---|---|
--output | file required output | Output file with cluster assignments. Contains original intervals with an additional column showing the cluster ID for each interval. Intervals in the same cluster have the same cluster ID number. |
Clustering Options
Name | Type & Properties | Description |
|---|---|---|
--distance -d | integer | Maximum distance between features for clustering. **Default:** 0 (only overlapping and book-ended features clustered) **Positive values:** Cluster features within specified distance **Use case:** Group nearby but non-overlapping features |
--strand -s | boolean_true | Force strandedness in clustering. **Default:** Clustering ignores strand information **When enabled:** Only cluster features on the same strand **Use case:** Strand-specific analysis of genomic features |
Run this component
Run the following command to execute this component with Nextflow:
cat > params.yaml <<'EOM'
output: "$id.$key.output.bed"
distance: [ 0 ]
id: "run"
publish_dir: "output/"
EOM
nextflow run https://packages.viash-hub.com/vsh/biobox.git \
-revision v0.4.1 \
-main-script target/nextflow/bedtools/bedtools_cluster/main.nf \
-params-file params.yaml Relationships
Used by
0 relationships
No components use this component.
Current component
bedtools/bedtools_clusterbiobox v0.4.1
Uses
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