Coverage Bed

coverage-bed

Quick Start

• Command: coverageBed -a targets.bed -b features.bed [options]
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/coverageBed
• Full reference: See references/help.md

When To Use This Tool

• Measure how much of each A interval is covered by features in B.
• Report per-interval overlap count, covered bases, and coverage fraction.
• Emit mean depth, histograms, or per-position depth over A intervals.
• Add strand-aware and overlap-fraction constraints before summarizing coverage.

Common Patterns

# 1) Default per-interval coverage summary
coverageBed \
  -a exons.bed \
  -b reads.bed

# 2) Report mean depth per target interval
coverageBed \
  -a exons.bed \
  -b reads.bed \
  -mean

# 3) Emit a coverage histogram per interval
coverageBed \
  -a exons.bed \
  -b reads.bed \
  -hist

Recommended Workflow

1. Decide whether you need the default summary, -counts, -mean, -hist, or per-position -d output before wiring this into a pipeline.
2. Treat A as the reporting frame: every result is anchored to intervals in A, not B.
3. Add -s / -S, -f / -F, -r, or -e only when you mean to constrain which B overlaps count toward coverage.
4. Use -sorted plus -g for large sorted files when performance matters.

Guardrails

• Both -a and -b are required.
• The default output appends four fields to each A record: overlap count, covered bases in A, A length, and covered fraction.
• -d reports one-based positions after each full A record, which changes the output shape substantially.
• -hist emits per-feature histograms plus a global summary histogram, so downstream parsers must be histogram-aware.
• Prefer -h for help; GNU-style --help / --version calls on these wrappers are noisy.