Protocol for detecting germline copy number variants from whole-exome sequencing using agent-assisted Snakemake workflows

Germline copy number variants (gCNVs) are vital for diagnosing rare monogenic disorders. Here, we present a containerized, agent-assisted Snakemake protocol for detecting, annotating, and visualizing gCNVs from short-read whole-exome sequencing data. We describe steps for constructing baseline models, executing CNV calling, annotating variant pathogenicity using public datasets, and rendering interactive visual reports. This automated workflow simplifies routine management and ensures cross-platform reproducibility through a unified interface.