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cnv-annotation

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Annotate copy number variant segments with overlapping genes, dosage-sensitivity scores, cancer driver databases, population frequencies, and clinical-variant content. Covers bedtools/pybedtools interval intersection, AnnotSV comprehensive annotation and ranking, ClinGen haploinsufficiency/triplosensitivity scoring, gnomAD-SV/DGV frequency filtering, COSMIC Cancer Gene Census, and ClinVar overlap. Use when interpreting which genes a CNV affects, distinguishing the driver gene of a focal event from passengers, filtering against population CNVs, separating whole-gene from partial-gene overlap, or preparing CNVs for clinical classification.

When to use

• Interpreting which genes a CNV affects
• Distinguishing the driver gene of a focal event from passengers
• Filtering against population CNVs
• Separating whole-gene from partial-gene overlap
• Preparing CNVs for clinical classification
• Annotating CNVs with genes, dosage maps, population frequency, and clinical databases
• Tagging affected genes with dosage sensitivity and driver role

When not to use

• Constitutional CNV classification (assigning pathogenic/VUS/benign)
• Cohort-level recurrence and driver-peak identification

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