Configuration

DELLY (De La Vega et al.)

Delly (v1.1.6) as run in the cited comparison.

Overview

Delly (v1.1.6) as run in the cited comparison.

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

Evaluations and results

1 evaluation · 22 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: DELLY (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	0.127 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 Delly (v1.1.6) 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, C11; row 'Delly (v1.1.6)'; group 'deletions, 1-5 kb'; column Precision
Configuration: DELLY (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	0.25 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 Delly (v1.1.6) 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, E11; row 'Delly (v1.1.6)'; group 'duplications, 1-5 kb'; column Precision
Configuration: DELLY (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	0.758 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 Delly (v1.1.6) 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, G11; row 'Delly (v1.1.6)'; group 'deletions, 5-10 kb'; column Precision
Configuration: DELLY (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 Delly (v1.1.6) 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, I11; row 'Delly (v1.1.6)'; group 'duplications, 5-10 kb'; column Precision
Configuration: DELLY (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	0.533 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 Delly (v1.1.6) 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, K11; row 'Delly (v1.1.6)'; group 'deletions, 10-50 kb'; column Precision
Configuration: DELLY (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	0.4 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 Delly (v1.1.6) 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, M11; row 'Delly (v1.1.6)'; group 'duplications, 10-50 kb'; column Precision
Configuration: DELLY (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	0.084 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 Delly (v1.1.6) 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, O11; row 'Delly (v1.1.6)'; group 'deletions, 50 kb and over'; column Precision
Configuration: DELLY (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	0.0001 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 Delly (v1.1.6) 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, Q11; row 'Delly (v1.1.6)'; group 'duplications, 50 kb and over'; column Precision
Configuration: DELLY (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	0.201 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 Delly (v1.1.6) 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, S11; row 'Delly (v1.1.6)'; group 'deletions, all sizes'; column Precision
Configuration: DELLY (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	0.104 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 Delly (v1.1.6) 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, U11; row 'Delly (v1.1.6)'; group 'duplications, all sizes'; column Precision
Configuration: DELLY (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	0.19 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 Delly (v1.1.6) 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, W11; row 'Delly (v1.1.6)'; group 'deletions and duplications combined'; column Precision
Configuration: DELLY (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	0.959 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 Delly (v1.1.6) 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, B11; row 'Delly (v1.1.6)'; group 'deletions, 1-5 kb'; column Sensitivity
Configuration: DELLY (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	0.25 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 Delly (v1.1.6) 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, D11; row 'Delly (v1.1.6)'; group 'duplications, 1-5 kb'; column Sensitivity
Configuration: DELLY (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	0.862 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 Delly (v1.1.6) 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, F11; row 'Delly (v1.1.6)'; group 'deletions, 5-10 kb'; column Sensitivity
Configuration: DELLY (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 Delly (v1.1.6) 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, H11; row 'Delly (v1.1.6)'; group 'duplications, 5-10 kb'; column Sensitivity
Configuration: DELLY (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	0.889 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 Delly (v1.1.6) 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, J11; row 'Delly (v1.1.6)'; group 'deletions, 10-50 kb'; column Sensitivity
Configuration: DELLY (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 Delly (v1.1.6) 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, L11; row 'Delly (v1.1.6)'; group 'duplications, 10-50 kb'; column Sensitivity
Configuration: DELLY (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 Delly (v1.1.6) 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, N11; row 'Delly (v1.1.6)'; group 'deletions, 50 kb and over'; column Sensitivity
Configuration: DELLY (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 Delly (v1.1.6) 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, P11; row 'Delly (v1.1.6)'; group 'duplications, 50 kb and over'; column Sensitivity
Configuration: DELLY (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	0.832 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 Delly (v1.1.6) 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, R11; row 'Delly (v1.1.6)'; group 'deletions, all sizes'; column Sensitivity
Configuration: DELLY (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	0.369 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 Delly (v1.1.6) 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, T11; row 'Delly (v1.1.6)'; group 'duplications, all sizes'; column Sensitivity
Configuration: DELLY (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	0.773 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 Delly (v1.1.6) 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, V11; row 'Delly (v1.1.6)'; group 'deletions and duplications combined'; column Sensitivity

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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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Stable ID: cnv-20261009-config-delavega2025-delly

areas: dna-genomes
contexts: clinical_research
method types: conventional_pipeline
reported name: Delly (v1.1.6)
version: Table S3 prints v1.1.6; Methods 2.3 prints v1.6
protocol: Default settings from DRAGEN multi-genome BAM
foundation model eligible: false

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configuration of: DELLY
system: Delly (v1.1.6) on HG002 exon-overlap benchmark

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