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.

Type

bash_script

License

MIT

Keywords

genomics

intervals

clustering

overlap

proximity

grouping

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.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

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

Name

Type & Properties

--input

-i

file

required

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.

Name

Type & Properties

--output

file

required

output

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

Name

Type & Properties

--distance

-d

integer

--strand

-s

boolean_true