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bio-genome-intervals-coverage-analysis - Calculate depth and coverage across genomic intervals

Calculate read depth and coverage across genomic intervals using bedtools, generate bedGraph files, compute per-base depth, and summarize statistics.

Tags

Updated: 2026-09-19
bedtoolsgenomecovcoveragebedgraphgenomics

Capabilities

Generate bedGraph filesCompute per-base coverage depthCalculate feature coverage statisticsCount reads across multiple BAMs

Typical Inputs

BAM alignment filesBED interval filesGenome size files

Typical Outputs

bedGraph filesCoverage summary filesCoverage histogram files

What this skill does

  • Generate bedGraph files
  • Compute per-base coverage depth
  • Calculate feature coverage statistics
  • Count reads across multiple BAMs

Inputs

  • BAM alignment files
  • BED interval files
  • Genome size files

Outputs

  • bedGraph files
  • Coverage summary files
  • Coverage histogram files

Requirements

  • bedtools 2.31+
  • samtools 1.19+
  • numpy 1.26+
  • pandas 2.2+

Source

  • Spec: SKILL.md

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