merge-bed

name	merge-bed
description	Use when merging overlapping or book-ended intervals in BED/GFF/VCF files into single intervals.
disable-model-invocation	true
user-invocable	true

merge-bed

Quick Start

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

When To Use This Tool

• Collapse overlapping or book-ended intervals into nonredundant merged regions.
• Merge nearby intervals within a maximum gap using -d.
• Keep strand-specific merged blocks with -s or one chosen strand with -S.
• Summarize columns across merged blocks with -c and -o.

Common Patterns

# 1) Basic merge of sorted intervals
mergeBed \
  -i peaks.sorted.bed

# 2) Merge intervals within 500 bp on the same strand
mergeBed \
  -i exons.sorted.bed \
  -s \
  -d 500

# 3) Merge and summarize scores and names
mergeBed \
  -i peaks.sorted.bed \
  -c 4,5 \
  -o collapse,max

Recommended Workflow

1. Sort the input by chromosome and start coordinate before anything else.
2. Decide whether book-ended features should merge as-is (-d 0, the default) or whether you need a stricter / looser distance rule.
3. Add -s / -S only when strand is biologically meaningful for the interval type.
4. Use -c and -o explicitly if you need metadata preserved, because raw merge output only reports merged coordinates.

Guardrails

• Sorted input is mandatory; unsorted files will produce wrong output.
• -d 0 merges both overlapping and directly book-ended intervals; many users forget the book-ended part.
• Negative -d values enforce a minimum required overlap rather than a gap tolerance.
• If you provide multiple -c columns and multiple -o operations, their counts must align unless you intentionally rely on the single-column / single-op broadcast behavior.
• Prefer -h for help; --version is not cleanly supported on this wrapper.