bio-genome-intervals-coverage-analysis - Analyze sequencing depth and coverage across genomic regions
Computes and interprets sequencing depth, breadth, coverage distributions, callable regions, and target-capture uniformity using mosdepth, bedtools, and samtools.
Tags
Updated: 2026-10-03Capabilities
Typical Inputs
Typical Outputs
What this skill does
- Compute windowed sequencing depth
- Measure breadth at thresholds
- Generate cumulative coverage curves
- Quantify coverage evenness
- Create bedGraph coverage tracks
- Define callable regions
- Summarize per-target coverage
- Assess capture uniformity
Inputs
- BAM alignment files
- Target BED intervals
- Reference genome
- MAPQ thresholds
- Callable depth thresholds
- Tool version information
Outputs
- Coverage summary metrics
- Cumulative coverage distributions
- Per-window coverage files
- Per-target coverage statistics
- BedGraph coverage tracks
- Callable-region BED files
- Coverage histograms
Requirements
- mosdepth 0.3+
- bedtools 2.31+
- samtools 1.19+
- pybedtools 0.10+
- numpy 1.26+
- BAM files with required indexes
- Reference genome for CRAM input