Protocol

Coriell virtual gene-panel CNV precision by exon count and length (De La Vega et al. Table 1)

Precision of DRAGEN modalities within a 184-gene virtual panel.

Overview

Precision of DRAGEN modalities within a 184-gene virtual panel.

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2 recorded evaluations, 12 metric rows. A comparison chart has not yet been validated for these results. The table retains the individual findings and their sources.

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Results

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All evaluations

2 evaluations · 12 results. Different protocols are not a single leaderboard.

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Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: DRAGEN 4.2 high-sensitivity mode (HS)	Protocol: Coriell virtual gene-panel CNV precision by exon count and length (De La Vega et al. Table 1) Dataset: 25 Coriell cell lines with documented CNVs, 184-gene virtual panel	8% precision percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Results 3.1 paragraph 5 says CNVnator and Cue were unable to detect events of 1-5 kb, but Supplemental Table 3 prints CNVnator 1-5 kb deletion sensitivity 0.3098 and precision 0.4207 (B9, C9). Results 3.1 paragraph 3 says Delly had the lowest precision, but Table S3 prints lower combined precision for Lumpy (W13 0.0107) than Delly (W11 0.1902). The prose may describe Figures 1 and 3 rather than the table; this was not checked. Table values are recorded.Benchmarking of germline copy number variant callers from whole genome sequencing data for clinical applications · Results 3.1 paragraphs 3 and 5 versus Supplemental_Table_3.xlsx B9, C9, W11, W13 Methods, coverage and source HS on Coriell virtual panel cnv-20261009-protocol-delavega2025-coriell-virtual-panel Aggregation: Not reported Benchmarking of germline copy number variant callers from whole genome sequencing data for clinical applications · Table 1, row '1' / '0.5–1', column 'Precision HS (%)' (exons spanned block)
Configuration: DRAGEN 4.2 high-sensitivity mode (HS)	Protocol: Coriell virtual gene-panel CNV precision by exon count and length (De La Vega et al. Table 1) Dataset: 25 Coriell cell lines with documented CNVs, 184-gene virtual panel	10% precision percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Results 3.1 paragraph 5 says CNVnator and Cue were unable to detect events of 1-5 kb, but Supplemental Table 3 prints CNVnator 1-5 kb deletion sensitivity 0.3098 and precision 0.4207 (B9, C9). Results 3.1 paragraph 3 says Delly had the lowest precision, but Table S3 prints lower combined precision for Lumpy (W13 0.0107) than Delly (W11 0.1902). The prose may describe Figures 1 and 3 rather than the table; this was not checked. Table values are recorded.Benchmarking of germline copy number variant callers from whole genome sequencing data for clinical applications · Results 3.1 paragraphs 3 and 5 versus Supplemental_Table_3.xlsx B9, C9, W11, W13 Methods, coverage and source HS on Coriell virtual panel cnv-20261009-protocol-delavega2025-coriell-virtual-panel Aggregation: Not reported Benchmarking of germline copy number variant callers from whole genome sequencing data for clinical applications · Table 1, row '2–5' / '1–10', column 'Precision HS (%)' (exons spanned block)
Configuration: DRAGEN 4.2 high-sensitivity mode (HS)	Protocol: Coriell virtual gene-panel CNV precision by exon count and length (De La Vega et al. Table 1) Dataset: 25 Coriell cell lines with documented CNVs, 184-gene virtual panel	1% precision percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Results 3.1 paragraph 5 says CNVnator and Cue were unable to detect events of 1-5 kb, but Supplemental Table 3 prints CNVnator 1-5 kb deletion sensitivity 0.3098 and precision 0.4207 (B9, C9). Results 3.1 paragraph 3 says Delly had the lowest precision, but Table S3 prints lower combined precision for Lumpy (W13 0.0107) than Delly (W11 0.1902). The prose may describe Figures 1 and 3 rather than the table; this was not checked. Table values are recorded.Benchmarking of germline copy number variant callers from whole genome sequencing data for clinical applications · Results 3.1 paragraphs 3 and 5 versus Supplemental_Table_3.xlsx B9, C9, W11, W13 Methods, coverage and source HS on Coriell virtual panel cnv-20261009-protocol-delavega2025-coriell-virtual-panel Aggregation: Not reported Benchmarking of germline copy number variant callers from whole genome sequencing data for clinical applications · Table 1, row '>5' / '>10', column 'Precision HS (%)' (exons spanned block)
Configuration: DRAGEN 4.2 high-sensitivity mode (HS)	Protocol: Coriell virtual gene-panel CNV precision by exon count and length (De La Vega et al. Table 1) Dataset: 25 Coriell cell lines with documented CNVs, 184-gene virtual panel	100% precision percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Results 3.1 paragraph 5 says CNVnator and Cue were unable to detect events of 1-5 kb, but Supplemental Table 3 prints CNVnator 1-5 kb deletion sensitivity 0.3098 and precision 0.4207 (B9, C9). Results 3.1 paragraph 3 says Delly had the lowest precision, but Table S3 prints lower combined precision for Lumpy (W13 0.0107) than Delly (W11 0.1902). The prose may describe Figures 1 and 3 rather than the table; this was not checked. Table values are recorded.Benchmarking of germline copy number variant callers from whole genome sequencing data for clinical applications · Results 3.1 paragraphs 3 and 5 versus Supplemental_Table_3.xlsx B9, C9, W11, W13 Methods, coverage and source HS on Coriell virtual panel cnv-20261009-protocol-delavega2025-coriell-virtual-panel Aggregation: Not reported Benchmarking of germline copy number variant callers from whole genome sequencing data for clinical applications · Table 1, row '1' / '0.5–1', column 'Precision HS (%)' (CNV length block)
Configuration: DRAGEN 4.2 high-sensitivity mode (HS)	Protocol: Coriell virtual gene-panel CNV precision by exon count and length (De La Vega et al. Table 1) Dataset: 25 Coriell cell lines with documented CNVs, 184-gene virtual panel	30% precision percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Results 3.1 paragraph 5 says CNVnator and Cue were unable to detect events of 1-5 kb, but Supplemental Table 3 prints CNVnator 1-5 kb deletion sensitivity 0.3098 and precision 0.4207 (B9, C9). Results 3.1 paragraph 3 says Delly had the lowest precision, but Table S3 prints lower combined precision for Lumpy (W13 0.0107) than Delly (W11 0.1902). The prose may describe Figures 1 and 3 rather than the table; this was not checked. Table values are recorded.Benchmarking of germline copy number variant callers from whole genome sequencing data for clinical applications · Results 3.1 paragraphs 3 and 5 versus Supplemental_Table_3.xlsx B9, C9, W11, W13 Methods, coverage and source HS on Coriell virtual panel cnv-20261009-protocol-delavega2025-coriell-virtual-panel Aggregation: Not reported Benchmarking of germline copy number variant callers from whole genome sequencing data for clinical applications · Table 1, row '2–5' / '1–10', column 'Precision HS (%)' (CNV length block)
Configuration: DRAGEN 4.2 high-sensitivity mode (HS)	Protocol: Coriell virtual gene-panel CNV precision by exon count and length (De La Vega et al. Table 1) Dataset: 25 Coriell cell lines with documented CNVs, 184-gene virtual panel	2% precision percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Results 3.1 paragraph 5 says CNVnator and Cue were unable to detect events of 1-5 kb, but Supplemental Table 3 prints CNVnator 1-5 kb deletion sensitivity 0.3098 and precision 0.4207 (B9, C9). Results 3.1 paragraph 3 says Delly had the lowest precision, but Table S3 prints lower combined precision for Lumpy (W13 0.0107) than Delly (W11 0.1902). The prose may describe Figures 1 and 3 rather than the table; this was not checked. Table values are recorded.Benchmarking of germline copy number variant callers from whole genome sequencing data for clinical applications · Results 3.1 paragraphs 3 and 5 versus Supplemental_Table_3.xlsx B9, C9, W11, W13 Methods, coverage and source HS on Coriell virtual panel cnv-20261009-protocol-delavega2025-coriell-virtual-panel Aggregation: Not reported Benchmarking of germline copy number variant callers from whole genome sequencing data for clinical applications · Table 1, row '>5' / '>10', column 'Precision HS (%)' (CNV length block)
Configuration: DRAGEN 4.2 high-sensitivity mode with custom artifact filters (HS-F)	Protocol: Coriell virtual gene-panel CNV precision by exon count and length (De La Vega et al. Table 1) Dataset: 25 Coriell cell lines with documented CNVs, 184-gene virtual panel	100% precision percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Results 3.1 paragraph 5 says CNVnator and Cue were unable to detect events of 1-5 kb, but Supplemental Table 3 prints CNVnator 1-5 kb deletion sensitivity 0.3098 and precision 0.4207 (B9, C9). Results 3.1 paragraph 3 says Delly had the lowest precision, but Table S3 prints lower combined precision for Lumpy (W13 0.0107) than Delly (W11 0.1902). The prose may describe Figures 1 and 3 rather than the table; this was not checked. Table values are recorded.Benchmarking of germline copy number variant callers from whole genome sequencing data for clinical applications · Results 3.1 paragraphs 3 and 5 versus Supplemental_Table_3.xlsx B9, C9, W11, W13 Methods, coverage and source HS-F on Coriell virtual panel cnv-20261009-protocol-delavega2025-coriell-virtual-panel Aggregation: Not reported Benchmarking of germline copy number variant callers from whole genome sequencing data for clinical applications · Table 1, row '1' / '0.5–1', column 'Precision HS-F (%)' (exons spanned block)
Configuration: DRAGEN 4.2 high-sensitivity mode with custom artifact filters (HS-F)	Protocol: Coriell virtual gene-panel CNV precision by exon count and length (De La Vega et al. Table 1) Dataset: 25 Coriell cell lines with documented CNVs, 184-gene virtual panel	81% precision percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Results 3.1 paragraph 5 says CNVnator and Cue were unable to detect events of 1-5 kb, but Supplemental Table 3 prints CNVnator 1-5 kb deletion sensitivity 0.3098 and precision 0.4207 (B9, C9). Results 3.1 paragraph 3 says Delly had the lowest precision, but Table S3 prints lower combined precision for Lumpy (W13 0.0107) than Delly (W11 0.1902). The prose may describe Figures 1 and 3 rather than the table; this was not checked. Table values are recorded.Benchmarking of germline copy number variant callers from whole genome sequencing data for clinical applications · Results 3.1 paragraphs 3 and 5 versus Supplemental_Table_3.xlsx B9, C9, W11, W13 Methods, coverage and source HS-F on Coriell virtual panel cnv-20261009-protocol-delavega2025-coriell-virtual-panel Aggregation: Not reported Benchmarking of germline copy number variant callers from whole genome sequencing data for clinical applications · Table 1, row '2–5' / '1–10', column 'Precision HS-F (%)' (exons spanned block)
Configuration: DRAGEN 4.2 high-sensitivity mode with custom artifact filters (HS-F)	Protocol: Coriell virtual gene-panel CNV precision by exon count and length (De La Vega et al. Table 1) Dataset: 25 Coriell cell lines with documented CNVs, 184-gene virtual panel	68% precision percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Results 3.1 paragraph 5 says CNVnator and Cue were unable to detect events of 1-5 kb, but Supplemental Table 3 prints CNVnator 1-5 kb deletion sensitivity 0.3098 and precision 0.4207 (B9, C9). Results 3.1 paragraph 3 says Delly had the lowest precision, but Table S3 prints lower combined precision for Lumpy (W13 0.0107) than Delly (W11 0.1902). The prose may describe Figures 1 and 3 rather than the table; this was not checked. Table values are recorded.Benchmarking of germline copy number variant callers from whole genome sequencing data for clinical applications · Results 3.1 paragraphs 3 and 5 versus Supplemental_Table_3.xlsx B9, C9, W11, W13 Methods, coverage and source HS-F on Coriell virtual panel cnv-20261009-protocol-delavega2025-coriell-virtual-panel Aggregation: Not reported Benchmarking of germline copy number variant callers from whole genome sequencing data for clinical applications · Table 1, row '>5' / '>10', column 'Precision HS-F (%)' (exons spanned block)
Configuration: DRAGEN 4.2 high-sensitivity mode with custom artifact filters (HS-F)	Protocol: Coriell virtual gene-panel CNV precision by exon count and length (De La Vega et al. Table 1) Dataset: 25 Coriell cell lines with documented CNVs, 184-gene virtual panel	100% precision percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Results 3.1 paragraph 5 says CNVnator and Cue were unable to detect events of 1-5 kb, but Supplemental Table 3 prints CNVnator 1-5 kb deletion sensitivity 0.3098 and precision 0.4207 (B9, C9). Results 3.1 paragraph 3 says Delly had the lowest precision, but Table S3 prints lower combined precision for Lumpy (W13 0.0107) than Delly (W11 0.1902). The prose may describe Figures 1 and 3 rather than the table; this was not checked. Table values are recorded.Benchmarking of germline copy number variant callers from whole genome sequencing data for clinical applications · Results 3.1 paragraphs 3 and 5 versus Supplemental_Table_3.xlsx B9, C9, W11, W13 Methods, coverage and source HS-F on Coriell virtual panel cnv-20261009-protocol-delavega2025-coriell-virtual-panel Aggregation: Not reported Benchmarking of germline copy number variant callers from whole genome sequencing data for clinical applications · Table 1, row '1' / '0.5–1', column 'Precision HS-F (%)' (CNV length block)
Configuration: DRAGEN 4.2 high-sensitivity mode with custom artifact filters (HS-F)	Protocol: Coriell virtual gene-panel CNV precision by exon count and length (De La Vega et al. Table 1) Dataset: 25 Coriell cell lines with documented CNVs, 184-gene virtual panel	89% precision percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Results 3.1 paragraph 5 says CNVnator and Cue were unable to detect events of 1-5 kb, but Supplemental Table 3 prints CNVnator 1-5 kb deletion sensitivity 0.3098 and precision 0.4207 (B9, C9). Results 3.1 paragraph 3 says Delly had the lowest precision, but Table S3 prints lower combined precision for Lumpy (W13 0.0107) than Delly (W11 0.1902). The prose may describe Figures 1 and 3 rather than the table; this was not checked. Table values are recorded.Benchmarking of germline copy number variant callers from whole genome sequencing data for clinical applications · Results 3.1 paragraphs 3 and 5 versus Supplemental_Table_3.xlsx B9, C9, W11, W13 Methods, coverage and source HS-F on Coriell virtual panel cnv-20261009-protocol-delavega2025-coriell-virtual-panel Aggregation: Not reported Benchmarking of germline copy number variant callers from whole genome sequencing data for clinical applications · Table 1, row '2–5' / '1–10', column 'Precision HS-F (%)' (CNV length block)
Configuration: DRAGEN 4.2 high-sensitivity mode with custom artifact filters (HS-F)	Protocol: Coriell virtual gene-panel CNV precision by exon count and length (De La Vega et al. Table 1) Dataset: 25 Coriell cell lines with documented CNVs, 184-gene virtual panel	74% precision percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Results 3.1 paragraph 5 says CNVnator and Cue were unable to detect events of 1-5 kb, but Supplemental Table 3 prints CNVnator 1-5 kb deletion sensitivity 0.3098 and precision 0.4207 (B9, C9). Results 3.1 paragraph 3 says Delly had the lowest precision, but Table S3 prints lower combined precision for Lumpy (W13 0.0107) than Delly (W11 0.1902). The prose may describe Figures 1 and 3 rather than the table; this was not checked. Table values are recorded.Benchmarking of germline copy number variant callers from whole genome sequencing data for clinical applications · Results 3.1 paragraphs 3 and 5 versus Supplemental_Table_3.xlsx B9, C9, W11, W13 Methods, coverage and source HS-F on Coriell virtual panel cnv-20261009-protocol-delavega2025-coriell-virtual-panel Aggregation: Not reported Benchmarking of germline copy number variant callers from whole genome sequencing data for clinical applications · Table 1, row '>5' / '>10', column 'Precision HS-F (%)' (CNV length block)

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Benchmarking of germline copy number variant callers from whole genome sequencing data for clinical applications · Original source · Bioinformatics Advances 5(1):vbaf071, published 2025-04-10; PMC12005901 full-text XML

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Technical metadata and extraction receipts

Stable ID: cnv-20261009-protocol-delavega2025-coriell-virtual-panel

areas: dna-genomes
contexts: clinical_research
protocol: Exon-overlap and dosage-direction matching within the 184-gene panel; precision stratified by number of exons spanned and by event length.
version: Table 1
limitations: Truth set curated partly by visual inspection of the same data, which can favour the evaluated caller.; Filtering scheme for HS-F was designed on these genes; the authors note possible overfitting (Discussion paragraph 7).; Table 1 prints precision only; Results 3.2 states 100% sensitivity across strata in prose
missing metadata: denominator: reason: unreported

Related records

uses data: 25 Coriell cell lines with documented CNVs, 184-gene virtual panel
assessment: HS on Coriell virtual panel
assessment: HS-F on Coriell virtual panel
assessed by: Select a copy-number variant detection and characterisation workflow

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