cluster-bed

name	cluster-bed
description	Use when you need to cluster overlapping or nearby genomic intervals in BED, GFF, or VCF files into groups.
disable-model-invocation	true
user-invocable	true

cluster-bed

Quick Start

• Command: clusterBed -i intervals.bed [options]
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/clusterBed
• Full reference: See references/help.md

When To Use This Tool

• Assign intervals into overlap / proximity-based clusters while preserving each original record.
• Group peaks, exons, or other features by neighborhood without collapsing them into merged coordinates.
• Keep strand-specific cluster assignment with -s.
• Expand clusters to nearby but non-overlapping features with -d.

Common Patterns

# 1) Cluster overlapping or book-ended intervals
clusterBed \
  -i peaks.bed

# 2) Cluster intervals within 1000 bp
clusterBed \
  -i peaks.bed \
  -d 1000

# 3) Cluster on the same strand only
clusterBed \
  -i transcripts.bed \
  -s

Recommended Workflow

1. Use clusterBed when you need cluster IDs on original records, not merged coordinates.
2. Set -d deliberately based on the biological neighborhood you want to treat as one cluster.
3. Add -s only when strand is meaningful for the feature class.
4. Feed the appended cluster ID into downstream grouping, summarization, or visualization steps.

Guardrails

• This tool appends a cluster ID; it does not merge records the way mergeBed does.
• The default -d 0 clusters overlapping and book-ended intervals together.
• Cluster numbering depends on input order, so pre-sort input if you need stable IDs across reruns.
• -s prevents opposite-strand records from entering the same cluster.
• Prefer -h for help; GNU-style --help / --version calls on these wrappers are noisy.