cnvkit-copy-number

What problem does it solve?

This Skill automates the detection of somatic copy number variants (CNVs) from sequencing data, which is crucial for understanding cancer genomics and identifying potential therapeutic targets.

Core Features & Use Cases

• Somatic CNV Detection: Identifies amplifications and deletions in tumor samples using WES, WGS, or targeted panels.
• Purity & Ploidy Estimation: Estimates tumor purity and ploidy to refine CNV calls.
• Data Export: Generates output files in standard formats (VCF, SEG, BED) for downstream analysis and visualization.
• Use Case: Analyze a tumor-normal pair of WES samples to identify regions of amplification or homozygous deletion, and export these findings for visualization in cBioPortal.

Quick Start

Run the cnvkit.py batch command to perform a paired tumor/normal CNV analysis on your WES data.