WGS Copy Number Variation

Generated on 2026-05-13

Copy Number Variation

The DRAGEN Copy Number Variant (CNV) Pipeline can call CNV events using next-generation sequencing (NGS) data. This pipeline supports multiple applications in a single interface via the DRAGEN Host Software, including processing of whole-genome sequencing (WGS) data and whole-exome sequencing (WES) data. For more information, refer to the DRAGEN user guide for germline CNV calling.

DRAGEN: DRAGEN 4.5.4 | Truthset: HG002 NIST CNV v0.6 | Reference: GRCh38

Standard WGS CNV table (click to expand)

Subtype	Recall	Precision	F1-score
1kb-10kb	0.968	0.977	0.973
10kb-50kb	0.950	0.952	0.951
>50kb	1.000	1.000	1.000

CNV for Standard WGS

Cytogenomics Modality

Conventional cytogenomics methodologies typically focus on larger alterations than the ones provided by NGS analyses. The Cytogenomics modality for the CNV caller allows the user to visualize variants at different resolutions, aiming at providing a more flexible workspace for different use cases. For more information, refer to DRAGEN manual.

Cytogenomics CNV summary table (click to expand)

Group	TP	FN	Recall
DEL 25kb-1Mb	15	1	0.938
DEL >=1Mb	46	1	0.979
DUP 50kb-1Mb	10	0	1.000
DUP >=1Mb	29	1	0.967
AOH >=500kb	43	0	1.000
TOTAL	143	3	0.979

Cytogenomics CNV Recall by Group