annotate-bed

name	annotate-bed
description	Use when you need to annotate BED/GFF/VCF intervals with coverage depth and breadth from multiple feature files.
disable-model-invocation	true
user-invocable	true

annotate-bed

Quick Start

• Command: annotateBed -i intervals.bed -files file1.bed file2.bed ... [options]
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/annotateBed
• Full reference: See references/help.md

When To Use This Tool

• Annotate each interval in a primary file with coverage or overlap counts from multiple feature files.
• Summarize fraction covered, counts, or both across many annotation tracks at once.
• Compare how one set of intervals intersects promoters, exons, enhancers, blacklist regions, or similar catalogs.
• Restrict overlap accounting by strand with -s or -S.

Common Patterns

# 1) Annotate intervals by fractional coverage from two tracks
annotateBed \
  -i peaks.bed \
  -files promoters.bed enhancers.bed

# 2) Report counts instead of fraction covered
annotateBed \
  -i peaks.bed \
  -files promoters.bed enhancers.bed \
  -counts

# 3) Emit both counts and coverage with readable column names
annotateBed \
  -i peaks.bed \
  -files promoters.bed enhancers.bed \
  -names promoters enhancers \
  -both

Recommended Workflow

1. Pick a primary interval file whose row order you want to preserve in the output.
2. Decide whether the output should represent breadth (default), hit count (-counts), or both (-both).
3. Use -names so the header is interpretable when many annotation tracks are involved.
4. Validate a few intervals manually if the distinction between coverage fraction and feature count matters downstream.

Guardrails

• -i and -files are both required.
• -names should have one label per annotation file if you want a correct header.
• -counts and -both change the meaning and number of appended columns, so downstream parsers must know which mode you used.
• -s and -S are mutually exclusive.
• Prefer -h for help; GNU-style --help / --version calls on these wrappers produce noisy errors.