Protocol

HG002 exon-overlap CNV benchmark by event type and length (De La Vega et al. Table S3)

Clinical-style CNV scoring by coding-exon overlap and dosage direction.

Overview

Clinical-style CNV scoring by coding-exon overlap and dosage direction.

Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.

8 recorded evaluations, 176 metric rows. A comparison chart has not yet been validated for these results. The table retains the individual findings and their sources.

View coverage and remaining gaps across all benchmarks

Results

Results are available, but no reviewed comparison panel is linked in this release.

All evaluations

8 evaluations · 176 results. Different protocols are not a single leaderboard.

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Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

Applied filters: All linked evaluations

Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: CNVnator v0.4.1 (De La Vega et al.)	Protocol: HG002 exon-overlap CNV benchmark by event type and length (De La Vega et al. Table S3) Dataset: HG002 50x PCR-free WGS with GIAB SV v0.6 CNV truth and synthetic gene models	0.421 precision fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external 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 CNVnator (v0.4.1) on HG002 exon-overlap benchmark cnv-20261009-protocol-delavega2025-hg002-exon-overlap Aggregation: Not reported Benchmarking of germline copy number variant callers from whole genome sequencing data for clinical applications; De La Vega et al. 2025, Supplemental Table 3 · Supplemental Table 3, C9; row 'CNVnator (v0.4.1)'; group 'deletions, 1-5 kb'; column Precision
Configuration: CNVnator v0.4.1 (De La Vega et al.)	Protocol: HG002 exon-overlap CNV benchmark by event type and length (De La Vega et al. Table S3) Dataset: HG002 50x PCR-free WGS with GIAB SV v0.6 CNV truth and synthetic gene models	NA precision fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external 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 CNVnator (v0.4.1) on HG002 exon-overlap benchmark cnv-20261009-protocol-delavega2025-hg002-exon-overlap Aggregation: Not reported Benchmarking of germline copy number variant callers from whole genome sequencing data for clinical applications; De La Vega et al. 2025, Supplemental Table 3 · Supplemental Table 3, E9; row 'CNVnator (v0.4.1)'; group 'duplications, 1-5 kb'; column Precision
Configuration: CNVnator v0.4.1 (De La Vega et al.)	Protocol: HG002 exon-overlap CNV benchmark by event type and length (De La Vega et al. Table S3) Dataset: HG002 50x PCR-free WGS with GIAB SV v0.6 CNV truth and synthetic gene models	0.495 precision fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external 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 CNVnator (v0.4.1) on HG002 exon-overlap benchmark cnv-20261009-protocol-delavega2025-hg002-exon-overlap Aggregation: Not reported Benchmarking of germline copy number variant callers from whole genome sequencing data for clinical applications; De La Vega et al. 2025, Supplemental Table 3 · Supplemental Table 3, G9; row 'CNVnator (v0.4.1)'; group 'deletions, 5-10 kb'; column Precision
Configuration: CNVnator v0.4.1 (De La Vega et al.)	Protocol: HG002 exon-overlap CNV benchmark by event type and length (De La Vega et al. Table S3) Dataset: HG002 50x PCR-free WGS with GIAB SV v0.6 CNV truth and synthetic gene models	NA precision fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external 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 CNVnator (v0.4.1) on HG002 exon-overlap benchmark cnv-20261009-protocol-delavega2025-hg002-exon-overlap Aggregation: Not reported Benchmarking of germline copy number variant callers from whole genome sequencing data for clinical applications; De La Vega et al. 2025, Supplemental Table 3 · Supplemental Table 3, I9; row 'CNVnator (v0.4.1)'; group 'duplications, 5-10 kb'; column Precision
Configuration: CNVnator v0.4.1 (De La Vega et al.)	Protocol: HG002 exon-overlap CNV benchmark by event type and length (De La Vega et al. Table S3) Dataset: HG002 50x PCR-free WGS with GIAB SV v0.6 CNV truth and synthetic gene models	0.66 precision fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external 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 CNVnator (v0.4.1) on HG002 exon-overlap benchmark cnv-20261009-protocol-delavega2025-hg002-exon-overlap Aggregation: Not reported Benchmarking of germline copy number variant callers from whole genome sequencing data for clinical applications; De La Vega et al. 2025, Supplemental Table 3 · Supplemental Table 3, K9; row 'CNVnator (v0.4.1)'; group 'deletions, 10-50 kb'; column Precision
Configuration: CNVnator v0.4.1 (De La Vega et al.)	Protocol: HG002 exon-overlap CNV benchmark by event type and length (De La Vega et al. Table S3) Dataset: HG002 50x PCR-free WGS with GIAB SV v0.6 CNV truth and synthetic gene models	0.0769 precision fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external 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 CNVnator (v0.4.1) on HG002 exon-overlap benchmark cnv-20261009-protocol-delavega2025-hg002-exon-overlap Aggregation: Not reported Benchmarking of germline copy number variant callers from whole genome sequencing data for clinical applications; De La Vega et al. 2025, Supplemental Table 3 · Supplemental Table 3, M9; row 'CNVnator (v0.4.1)'; group 'duplications, 10-50 kb'; column Precision
Configuration: CNVnator v0.4.1 (De La Vega et al.)	Protocol: HG002 exon-overlap CNV benchmark by event type and length (De La Vega et al. Table S3) Dataset: HG002 50x PCR-free WGS with GIAB SV v0.6 CNV truth and synthetic gene models	0.134 precision fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external 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 CNVnator (v0.4.1) on HG002 exon-overlap benchmark cnv-20261009-protocol-delavega2025-hg002-exon-overlap Aggregation: Not reported Benchmarking of germline copy number variant callers from whole genome sequencing data for clinical applications; De La Vega et al. 2025, Supplemental Table 3 · Supplemental Table 3, O9; row 'CNVnator (v0.4.1)'; group 'deletions, 50 kb and over'; column Precision
Configuration: CNVnator v0.4.1 (De La Vega et al.)	Protocol: HG002 exon-overlap CNV benchmark by event type and length (De La Vega et al. Table S3) Dataset: HG002 50x PCR-free WGS with GIAB SV v0.6 CNV truth and synthetic gene models	0 precision fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external 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 CNVnator (v0.4.1) on HG002 exon-overlap benchmark cnv-20261009-protocol-delavega2025-hg002-exon-overlap Aggregation: Not reported Benchmarking of germline copy number variant callers from whole genome sequencing data for clinical applications; De La Vega et al. 2025, Supplemental Table 3 · Supplemental Table 3, Q9; row 'CNVnator (v0.4.1)'; group 'duplications, 50 kb and over'; column Precision
Configuration: CNVnator v0.4.1 (De La Vega et al.)	Protocol: HG002 exon-overlap CNV benchmark by event type and length (De La Vega et al. Table S3) Dataset: HG002 50x PCR-free WGS with GIAB SV v0.6 CNV truth and synthetic gene models	0.429 precision fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external 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 CNVnator (v0.4.1) on HG002 exon-overlap benchmark cnv-20261009-protocol-delavega2025-hg002-exon-overlap Aggregation: Not reported Benchmarking of germline copy number variant callers from whole genome sequencing data for clinical applications; De La Vega et al. 2025, Supplemental Table 3 · Supplemental Table 3, S9; row 'CNVnator (v0.4.1)'; group 'deletions, all sizes'; column Precision
Configuration: CNVnator v0.4.1 (De La Vega et al.)	Protocol: HG002 exon-overlap CNV benchmark by event type and length (De La Vega et al. Table S3) Dataset: HG002 50x PCR-free WGS with GIAB SV v0.6 CNV truth and synthetic gene models	0.0417 precision fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external 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 CNVnator (v0.4.1) on HG002 exon-overlap benchmark cnv-20261009-protocol-delavega2025-hg002-exon-overlap Aggregation: Not reported Benchmarking of germline copy number variant callers from whole genome sequencing data for clinical applications; De La Vega et al. 2025, Supplemental Table 3 · Supplemental Table 3, U9; row 'CNVnator (v0.4.1)'; group 'duplications, all sizes'; column Precision
Configuration: CNVnator v0.4.1 (De La Vega et al.)	Protocol: HG002 exon-overlap CNV benchmark by event type and length (De La Vega et al. Table S3) Dataset: HG002 50x PCR-free WGS with GIAB SV v0.6 CNV truth and synthetic gene models	0.306 precision fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external 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 CNVnator (v0.4.1) on HG002 exon-overlap benchmark cnv-20261009-protocol-delavega2025-hg002-exon-overlap Aggregation: Not reported Benchmarking of germline copy number variant callers from whole genome sequencing data for clinical applications; De La Vega et al. 2025, Supplemental Table 3 · Supplemental Table 3, W9; row 'CNVnator (v0.4.1)'; group 'deletions and duplications combined'; column Precision
Configuration: CNVnator v0.4.1 (De La Vega et al.)	Protocol: HG002 exon-overlap CNV benchmark by event type and length (De La Vega et al. Table S3) Dataset: HG002 50x PCR-free WGS with GIAB SV v0.6 CNV truth and synthetic gene models	0.31 recall fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external 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 CNVnator (v0.4.1) on HG002 exon-overlap benchmark cnv-20261009-protocol-delavega2025-hg002-exon-overlap Aggregation: Not reported Benchmarking of germline copy number variant callers from whole genome sequencing data for clinical applications; De La Vega et al. 2025, Supplemental Table 3 · Supplemental Table 3, B9; row 'CNVnator (v0.4.1)'; group 'deletions, 1-5 kb'; column Sensitivity
Configuration: CNVnator v0.4.1 (De La Vega et al.)	Protocol: HG002 exon-overlap CNV benchmark by event type and length (De La Vega et al. Table S3) Dataset: HG002 50x PCR-free WGS with GIAB SV v0.6 CNV truth and synthetic gene models	0 recall fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external 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 CNVnator (v0.4.1) on HG002 exon-overlap benchmark cnv-20261009-protocol-delavega2025-hg002-exon-overlap Aggregation: Not reported Benchmarking of germline copy number variant callers from whole genome sequencing data for clinical applications; De La Vega et al. 2025, Supplemental Table 3 · Supplemental Table 3, D9; row 'CNVnator (v0.4.1)'; group 'duplications, 1-5 kb'; column Sensitivity
Configuration: CNVnator v0.4.1 (De La Vega et al.)	Protocol: HG002 exon-overlap CNV benchmark by event type and length (De La Vega et al. Table S3) Dataset: HG002 50x PCR-free WGS with GIAB SV v0.6 CNV truth and synthetic gene models	0.419 recall fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external 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 CNVnator (v0.4.1) on HG002 exon-overlap benchmark cnv-20261009-protocol-delavega2025-hg002-exon-overlap Aggregation: Not reported Benchmarking of germline copy number variant callers from whole genome sequencing data for clinical applications; De La Vega et al. 2025, Supplemental Table 3 · Supplemental Table 3, F9; row 'CNVnator (v0.4.1)'; group 'deletions, 5-10 kb'; column Sensitivity
Configuration: CNVnator v0.4.1 (De La Vega et al.)	Protocol: HG002 exon-overlap CNV benchmark by event type and length (De La Vega et al. Table S3) Dataset: HG002 50x PCR-free WGS with GIAB SV v0.6 CNV truth and synthetic gene models	NA recall fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external 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 CNVnator (v0.4.1) on HG002 exon-overlap benchmark cnv-20261009-protocol-delavega2025-hg002-exon-overlap Aggregation: Not reported Benchmarking of germline copy number variant callers from whole genome sequencing data for clinical applications; De La Vega et al. 2025, Supplemental Table 3 · Supplemental Table 3, H9; row 'CNVnator (v0.4.1)'; group 'duplications, 5-10 kb'; column Sensitivity
Configuration: CNVnator v0.4.1 (De La Vega et al.)	Protocol: HG002 exon-overlap CNV benchmark by event type and length (De La Vega et al. Table S3) Dataset: HG002 50x PCR-free WGS with GIAB SV v0.6 CNV truth and synthetic gene models	1 recall fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external 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 CNVnator (v0.4.1) on HG002 exon-overlap benchmark cnv-20261009-protocol-delavega2025-hg002-exon-overlap Aggregation: Not reported Benchmarking of germline copy number variant callers from whole genome sequencing data for clinical applications; De La Vega et al. 2025, Supplemental Table 3 · Supplemental Table 3, J9; row 'CNVnator (v0.4.1)'; group 'deletions, 10-50 kb'; column Sensitivity
Configuration: CNVnator v0.4.1 (De La Vega et al.)	Protocol: HG002 exon-overlap CNV benchmark by event type and length (De La Vega et al. Table S3) Dataset: HG002 50x PCR-free WGS with GIAB SV v0.6 CNV truth and synthetic gene models	0.5 recall fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external 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 CNVnator (v0.4.1) on HG002 exon-overlap benchmark cnv-20261009-protocol-delavega2025-hg002-exon-overlap Aggregation: Not reported Benchmarking of germline copy number variant callers from whole genome sequencing data for clinical applications; De La Vega et al. 2025, Supplemental Table 3 · Supplemental Table 3, L9; row 'CNVnator (v0.4.1)'; group 'duplications, 10-50 kb'; column Sensitivity
Configuration: CNVnator v0.4.1 (De La Vega et al.)	Protocol: HG002 exon-overlap CNV benchmark by event type and length (De La Vega et al. Table S3) Dataset: HG002 50x PCR-free WGS with GIAB SV v0.6 CNV truth and synthetic gene models	1 recall fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external 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 CNVnator (v0.4.1) on HG002 exon-overlap benchmark cnv-20261009-protocol-delavega2025-hg002-exon-overlap Aggregation: Not reported Benchmarking of germline copy number variant callers from whole genome sequencing data for clinical applications; De La Vega et al. 2025, Supplemental Table 3 · Supplemental Table 3, N9; row 'CNVnator (v0.4.1)'; group 'deletions, 50 kb and over'; column Sensitivity
Configuration: CNVnator v0.4.1 (De La Vega et al.)	Protocol: HG002 exon-overlap CNV benchmark by event type and length (De La Vega et al. Table S3) Dataset: HG002 50x PCR-free WGS with GIAB SV v0.6 CNV truth and synthetic gene models	NA recall fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external 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 CNVnator (v0.4.1) on HG002 exon-overlap benchmark cnv-20261009-protocol-delavega2025-hg002-exon-overlap Aggregation: Not reported Benchmarking of germline copy number variant callers from whole genome sequencing data for clinical applications; De La Vega et al. 2025, Supplemental Table 3 · Supplemental Table 3, P9; row 'CNVnator (v0.4.1)'; group 'duplications, 50 kb and over'; column Sensitivity
Configuration: CNVnator v0.4.1 (De La Vega et al.)	Protocol: HG002 exon-overlap CNV benchmark by event type and length (De La Vega et al. Table S3) Dataset: HG002 50x PCR-free WGS with GIAB SV v0.6 CNV truth and synthetic gene models	0.357 recall fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external 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 CNVnator (v0.4.1) on HG002 exon-overlap benchmark cnv-20261009-protocol-delavega2025-hg002-exon-overlap Aggregation: Not reported Benchmarking of germline copy number variant callers from whole genome sequencing data for clinical applications; De La Vega et al. 2025, Supplemental Table 3 · Supplemental Table 3, R9; row 'CNVnator (v0.4.1)'; group 'deletions, all sizes'; column Sensitivity
Configuration: CNVnator v0.4.1 (De La Vega et al.)	Protocol: HG002 exon-overlap CNV benchmark by event type and length (De La Vega et al. Table S3) Dataset: HG002 50x PCR-free WGS with GIAB SV v0.6 CNV truth and synthetic gene models	0.1 recall fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external 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 CNVnator (v0.4.1) on HG002 exon-overlap benchmark cnv-20261009-protocol-delavega2025-hg002-exon-overlap Aggregation: Not reported Benchmarking of germline copy number variant callers from whole genome sequencing data for clinical applications; De La Vega et al. 2025, Supplemental Table 3 · Supplemental Table 3, T9; row 'CNVnator (v0.4.1)'; group 'duplications, all sizes'; column Sensitivity
Configuration: CNVnator v0.4.1 (De La Vega et al.)	Protocol: HG002 exon-overlap CNV benchmark by event type and length (De La Vega et al. Table S3) Dataset: HG002 50x PCR-free WGS with GIAB SV v0.6 CNV truth and synthetic gene models	0.322 recall fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external 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 CNVnator (v0.4.1) on HG002 exon-overlap benchmark cnv-20261009-protocol-delavega2025-hg002-exon-overlap Aggregation: Not reported Benchmarking of germline copy number variant callers from whole genome sequencing data for clinical applications; De La Vega et al. 2025, Supplemental Table 3 · Supplemental Table 3, V9; row 'CNVnator (v0.4.1)'; group 'deletions and duplications combined'; column Sensitivity
Configuration: Cue, cue.v2.pt model (De La Vega et al.)	Protocol: HG002 exon-overlap CNV benchmark by event type and length (De La Vega et al. Table S3) Dataset: HG002 50x PCR-free WGS with GIAB SV v0.6 CNV truth and synthetic gene models	NA precision fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external 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 Cue (cue.v2.pt model) on HG002 exon-overlap benchmark cnv-20261009-protocol-delavega2025-hg002-exon-overlap Aggregation: Not reported Benchmarking of germline copy number variant callers from whole genome sequencing data for clinical applications; De La Vega et al. 2025, Supplemental Table 3 · Supplemental Table 3, C10; row 'Cue (cue.v2.pt model)'; group 'deletions, 1-5 kb'; column Precision
Configuration: Cue, cue.v2.pt model (De La Vega et al.)	Protocol: HG002 exon-overlap CNV benchmark by event type and length (De La Vega et al. Table S3) Dataset: HG002 50x PCR-free WGS with GIAB SV v0.6 CNV truth and synthetic gene models	0 precision fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external 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 Cue (cue.v2.pt model) on HG002 exon-overlap benchmark cnv-20261009-protocol-delavega2025-hg002-exon-overlap Aggregation: Not reported Benchmarking of germline copy number variant callers from whole genome sequencing data for clinical applications; De La Vega et al. 2025, Supplemental Table 3 · Supplemental Table 3, E10; row 'Cue (cue.v2.pt model)'; group 'duplications, 1-5 kb'; column Precision
Configuration: Cue, cue.v2.pt model (De La Vega et al.)	Protocol: HG002 exon-overlap CNV benchmark by event type and length (De La Vega et al. Table S3) Dataset: HG002 50x PCR-free WGS with GIAB SV v0.6 CNV truth and synthetic gene models	1 precision fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external 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 Cue (cue.v2.pt model) on HG002 exon-overlap benchmark cnv-20261009-protocol-delavega2025-hg002-exon-overlap Aggregation: Not reported Benchmarking of germline copy number variant callers from whole genome sequencing data for clinical applications; De La Vega et al. 2025, Supplemental Table 3 · Supplemental Table 3, G10; row 'Cue (cue.v2.pt model)'; group 'deletions, 5-10 kb'; column Precision

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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
De La Vega et al. 2025, Supplemental Table 3 · Original source · Supplemental_Table_3.xlsx inside vbaf071_supplementary_data.zip

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Technical metadata and extraction receipts

Stable ID: cnv-20261009-protocol-delavega2025-hg002-exon-overlap

areas: dna-genomes
contexts: clinical_research
protocol: True positive: call overlaps at least 1 bp of a coding exon of a canonical or synthetic transcript (plus 15 bp intronic) and matches dosage direction; multi-exon events adjusted to avoid double counting; other calls false positive. Sensitivity and precision by GA4GH definitions. Strata by type and length as printed in Table S3.
version: Supplemental Table 3
limitations: Single sample; truth relies on GIAB v0.6 and synthetic gene models placed by the authors.; Breakpoint accuracy and event length overlap are not scored.; Authors include employees of Tempus and Illumina (DRAGEN vendor), per the conflict-of-interest statement.
missing metadata: denominator: reason: unreported; note: Per-stratum counts unreported; metric implementation: reason: unreported; note: Evaluation code not identified in the article

Related records

uses data: HG002 50x PCR-free WGS with GIAB SV v0.6 CNV truth and synthetic gene models
assessment: CNVnator (v0.4.1) on HG002 exon-overlap benchmark
assessment: Cue (cue.v2.pt model) on HG002 exon-overlap benchmark
assessment: Delly (v1.1.6) on HG002 exon-overlap benchmark
assessment: Dragen v4.2 on HG002 exon-overlap benchmark
assessment: Dragen v4.2 HS on HG002 exon-overlap benchmark
assessment: Dragen v4.2 HS + Filters on HG002 exon-overlap benchmark
assessment: Lumpy on HG002 exon-overlap benchmark
assessment: Parliament 2 on HG002 exon-overlap benchmark
assessed by: Select a copy-number variant detection and characterisation workflow

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