CNVkit

Overview

CNVkit is an open-source toolkit for copy-number variant (CNV) detection from targeted DNA sequencing or whole-exome/whole-genome sequencing data. It estimates read depth in on-target and off-target regions, normalizes against a pooled reference, and infers log2 copy-number ratios and segmented CNV calls. CNVkit is widely used in cancer genomics pipelines for somatic CNA profiling.

Used by

• Applied to detect somatic copy-number alterations in endometrial polyps against a pooled normal reference of 18 matched bloods; identified chromosomal rearrangement-associated CNAs involving HMGA1/HMGA2 loci PMID:28445112

Notes

• Requires a matched or pooled normal reference for somatic calling.
• Supports WGS, WES, and targeted panel data.
• Outputs segmented log2-ratio profiles and can call focal amplifications and deletions.

Sources

• PMID:28445112

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