| 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
genomeCoverageBed \
-i reads.bed \
-g genome.txt
genomeCoverageBed \
-ibam reads.sorted.bam \
-bga > coverage.bedgraph
genomeCoverageBed \
-ibam reads.sorted.bam \
-dz
Recommended Workflow
- Choose the reporting mode first: histogram (
default), BedGraph (-bg / -bga), or depth (-d / -dz).
- For BED-like input, provide a valid genome file; for BAM input, position-sort the BAM before running coverage.
- Use
-split when spliced or blocked intervals should contribute as separate covered blocks.
- 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.
