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cnv-caller-plotter

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Detect copy number variations from whole genome sequencing data and generate publication-quality genome-wide CNV plots. Supports CNV calling, segmentation, and visualization for cancer genomics and rare disease analysis.

scientific-skills/Data Analysis/cnv-caller-plotter/SKILL.md

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> **Source**: [https://github.com/aipoch/medical-research-skills](https://github.com/aipoch/medical-research-skills)

# CNV Caller & Plotter

Detect copy number variations (CNVs) from whole genome sequencing (WGS) data and generate genome-wide visualization plots for cancer genomics, rare disease analysis, and population genetics studies. Provides CNV calling, segmentation analysis, and publication-ready visualization.

**Key Capabilities:**
- **CNV Detection from WGS**: Identify copy number gains and losses from aligned sequencing data
- **Genomic Segmentation**: Divide genome into bins/windows for copy number estimation
- **Flexible Input Support**: Process BAM, VCF, and other standard genomics formats
- **Publication-Quality Plots**: Generate genome-wide CNV profiles in PNG, PDF, or SVG formats
- **Standard Output Formats**: Export CNV calls in BED format for downstream analysis

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