genome-coverage-bed

name	genome-coverage-bed
description	Use when computing genome-wide coverage from BED/GFF/VCF or BAM files, generating coverage histograms, BedGraph tracks, or per-position depth reports.
disable-model-invocation	true
user-invocable	true

genome-coverage-bed

Quick Start

• Command: genomeCoverageBed -i features.bed -g genome.txt [options] or genomeCoverageBed -ibam reads.bam [options]
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/genomeCoverageBed
• Full reference: See references/help.md

When To Use This Tool

• Compute genome-wide coverage histograms from interval or BAM input.
• Generate BedGraph tracks with -bg or -bga for browser visualization.
• Emit per-base depth with -d or sparse zero-based depth with -dz.
• Normalize coverage by scale factor, strand, fragment model, or split alignment behavior.

Common Patterns

# 1) Default genome-wide histogram from BED intervals
genomeCoverageBed \
  -i reads.bed \
  -g genome.txt

# 2) BedGraph including zero-coverage intervals
genomeCoverageBed \
  -ibam reads.sorted.bam \
  -bga > coverage.bedgraph

# 3) Zero-based depth for non-zero positions only
genomeCoverageBed \
  -ibam reads.sorted.bam \
  -dz

Recommended Workflow

1. Choose the reporting mode first: histogram (default), BedGraph (-bg / -bga), or depth (-d / -dz).
2. For BED-like input, provide a valid genome file; for BAM input, position-sort the BAM before running coverage.
3. Use -split when spliced or blocked intervals should contribute as separate covered blocks.
4. Add -scale, -strand, -pc, -5, or -3 only when the biological interpretation of coverage depends on those choices.

Guardrails

• -g is required unless you use -ibam.
• BAM input must be position-sorted; BED input must be grouped by chromosome.
• -bga includes zero-coverage intervals, whereas -bg omits them.
• -d is one-based and reports every genomic position; -dz is zero-based and reports only non-zero positions.
• -trackline is convenient for browser upload, but that first line must be removed before BedGraph-to-BigWig conversion.