Evaluation

Dragen v4.2 HS + Filters on HG002 exon-overlap benchmark

Published CNV caller comparison; transcribed, not reproduced.

Research readiness

These checks assess whether the evidence supports a reproducible investigation. A source-checked score alone does not meet these requirements.

Release 2026-10-09-9307685239b3 · Evidence verified: Not verified

Evidence incomplete

Replay metrics

Exact outcomes, predictions, identifiers and evaluator are connected.

Missing or unresolved evidence

No verified artifact manifest is linked to this exact record.
artifact hashes: verification is missing
join integrity: verification is missing
score semantics: verification is missing
metric replay: verification is missing

Verified: Not verified

Evidence incomplete

Investigate discrepancies

Replay evidence includes annotations and an assessment of dependence. Unknown independence permits descriptive analysis only.

Missing or unresolved evidence

No verified artifact manifest is linked to this exact record.
artifact hashes: verification is missing
join integrity: verification is missing
score semantics: verification is missing
metric replay: verification is missing
annotations: verification is missing
dependence: verification is missing

Verified: Not verified

Evidence incomplete

Run locally

A pinned recipe describes the inputs, environment and resource requirements.

Missing or unresolved evidence

No verified artifact manifest is linked to this exact record.
artifact hashes: verification is missing
join integrity: verification is missing
score semantics: verification is missing
recipe pinned: verification is missing
resource estimate: verification is missing

Verified: Not verified

Evidence incomplete

Validate independently

Separate data and exposure records support an independent test.

Missing or unresolved evidence

No verified artifact manifest is linked to this exact record.
artifact hashes: verification is missing
join integrity: verification is missing
score semantics: verification is missing
independent validation: verification is missing
overlap checked: verification is missing

Verified: Not verified

Readiness describes the evidence in this release. Availability on your computer is checked separately when an investigation runs. Existing data exposure can prevent independent validation even when files are available.

Artifacts and reproduction

No verified artifact manifest is connected to this record yet. The gaps above identify what is needed before analysis can begin.

Read reviewed discrepancy investigations

Evaluation results

1 evaluation · 22 results. Different protocols are not a single leaderboard.

Filter evaluations

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: DRAGEN 4.2 high-sensitivity mode with custom artifact filters (HS-F)	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	0.949 precision fraction · 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 Dragen v4.2 HS + Filters 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, C6; row 'Dragen v4.2 HS + Filters'; group 'deletions, 1-5 kb'; column Precision
Configuration: DRAGEN 4.2 high-sensitivity mode with custom artifact filters (HS-F)	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	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 Dragen v4.2 HS + Filters 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, E6; row 'Dragen v4.2 HS + Filters'; group 'duplications, 1-5 kb'; column Precision
Configuration: DRAGEN 4.2 high-sensitivity mode with custom artifact filters (HS-F)	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	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 Dragen v4.2 HS + Filters 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, G6; row 'Dragen v4.2 HS + Filters'; group 'deletions, 5-10 kb'; column Precision
Configuration: DRAGEN 4.2 high-sensitivity mode with custom artifact filters (HS-F)	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	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 Dragen v4.2 HS + Filters 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, I6; row 'Dragen v4.2 HS + Filters'; group 'duplications, 5-10 kb'; column Precision
Configuration: DRAGEN 4.2 high-sensitivity mode with custom artifact filters (HS-F)	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	0.68 precision fraction · 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 Dragen v4.2 HS + Filters 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, K6; row 'Dragen v4.2 HS + Filters'; group 'deletions, 10-50 kb'; column Precision
Configuration: DRAGEN 4.2 high-sensitivity mode with custom artifact filters (HS-F)	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	0.182 precision fraction · 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 Dragen v4.2 HS + Filters 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, M6; row 'Dragen v4.2 HS + Filters'; group 'duplications, 10-50 kb'; column Precision
Configuration: DRAGEN 4.2 high-sensitivity mode with custom artifact filters (HS-F)	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	0.183 precision fraction · 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 Dragen v4.2 HS + Filters 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, O6; row 'Dragen v4.2 HS + Filters'; group 'deletions, 50 kb and over'; column Precision
Configuration: DRAGEN 4.2 high-sensitivity mode with custom artifact filters (HS-F)	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	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 Dragen v4.2 HS + Filters 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, Q6; row 'Dragen v4.2 HS + Filters'; group 'duplications, 50 kb and over'; column Precision
Configuration: DRAGEN 4.2 high-sensitivity mode with custom artifact filters (HS-F)	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	0.776 precision fraction · 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 Dragen v4.2 HS + Filters 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, S6; row 'Dragen v4.2 HS + Filters'; group 'deletions, all sizes'; column Precision
Configuration: DRAGEN 4.2 high-sensitivity mode with custom artifact filters (HS-F)	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	0.136 precision fraction · 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 Dragen v4.2 HS + Filters 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, U6; row 'Dragen v4.2 HS + Filters'; group 'duplications, all sizes'; column Precision
Configuration: DRAGEN 4.2 high-sensitivity mode with custom artifact filters (HS-F)	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	0.621 precision fraction · 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 Dragen v4.2 HS + Filters 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, W6; row 'Dragen v4.2 HS + Filters'; group 'deletions and duplications combined'; column Precision
Configuration: DRAGEN 4.2 high-sensitivity mode with custom artifact filters (HS-F)	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	0.822 recall fraction · 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 Dragen v4.2 HS + Filters 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, B6; row 'Dragen v4.2 HS + Filters'; group 'deletions, 1-5 kb'; column Sensitivity
Configuration: DRAGEN 4.2 high-sensitivity mode with custom artifact filters (HS-F)	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	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 Dragen v4.2 HS + Filters 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, D6; row 'Dragen v4.2 HS + Filters'; group 'duplications, 1-5 kb'; column Sensitivity
Configuration: DRAGEN 4.2 high-sensitivity mode with custom artifact filters (HS-F)	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	0.926 recall fraction · 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 Dragen v4.2 HS + Filters 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, F6; row 'Dragen v4.2 HS + Filters'; group 'deletions, 5-10 kb'; column Sensitivity
Configuration: DRAGEN 4.2 high-sensitivity mode with custom artifact filters (HS-F)	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	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 Dragen v4.2 HS + Filters 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, H6; row 'Dragen v4.2 HS + Filters'; group 'duplications, 5-10 kb'; column Sensitivity
Configuration: DRAGEN 4.2 high-sensitivity mode with custom artifact filters (HS-F)	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	0.895 recall fraction · 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 Dragen v4.2 HS + Filters 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, J6; row 'Dragen v4.2 HS + Filters'; group 'deletions, 10-50 kb'; column Sensitivity
Configuration: DRAGEN 4.2 high-sensitivity mode with custom artifact filters (HS-F)	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	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 Dragen v4.2 HS + Filters 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, L6; row 'Dragen v4.2 HS + Filters'; group 'duplications, 10-50 kb'; column Sensitivity
Configuration: DRAGEN 4.2 high-sensitivity mode with custom artifact filters (HS-F)	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	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 Dragen v4.2 HS + Filters 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, N6; row 'Dragen v4.2 HS + Filters'; group 'deletions, 50 kb and over'; column Sensitivity
Configuration: DRAGEN 4.2 high-sensitivity mode with custom artifact filters (HS-F)	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	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 Dragen v4.2 HS + Filters 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, P6; row 'Dragen v4.2 HS + Filters'; group 'duplications, 50 kb and over'; column Sensitivity
Configuration: DRAGEN 4.2 high-sensitivity mode with custom artifact filters (HS-F)	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	0.825 recall fraction · 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 Dragen v4.2 HS + Filters 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, R6; row 'Dragen v4.2 HS + Filters'; group 'deletions, all sizes'; column Sensitivity
Configuration: DRAGEN 4.2 high-sensitivity mode with custom artifact filters (HS-F)	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	0.3 recall fraction · 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 Dragen v4.2 HS + Filters 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, T6; row 'Dragen v4.2 HS + Filters'; group 'duplications, all sizes'; column Sensitivity
Configuration: DRAGEN 4.2 high-sensitivity mode with custom artifact filters (HS-F)	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	0.754 recall fraction · 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 Dragen v4.2 HS + Filters 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, V6; row 'Dragen v4.2 HS + Filters'; group 'deletions and duplications combined'; column Sensitivity

Source checking is not independent reproduction. Release 2026-10-09-9307685239b3.

Evaluation procedure

cnv-20261009-protocol-delavega2025-hg002-exon-overlap

Configuration: DRAGEN 4.2 high-sensitivity mode with custom artifact filters (HS-F)
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

origin: Author-reported evaluation
configuration: Primary source as retrieved 2026-10-09
protocol id: cnv-20261009-protocol-delavega2025-hg002-exon-overlap
dataset version: GIAB HG002 SV v0.6 GRCh37 plus synthetic genes
split: Single HG002 sample
population: 60 DEL and 10 DUP exon-overlapping truth events
inputs: 50x PCR-free WGS, DRAGEN multi-genome BAM on GRCh37
adaptation: Not reported
metric implementation: Not reported
aggregation: Single sample, per stratum
budget: Not reported

Metadata review: source checked. Unreported conditions prevent automatic comparisons.

Reproduction

Split: Single HG002 sample
Adaptation: Not reported
Scoring implementation: Not reported

No execution recipe has been verified for this exact configuration and evaluation. A benchmark's general instructions may use different inputs, splits or model settings.

Reproducing this published result requires matching its model configuration, data, split and scorer. Source checking or a successful smoke test does not establish score reproduction.

Evidence

Source checking verifies the cited claim or transcription. It does not establish independent reproduction.

Evidence table

Inspect claims, sources and review details

Trace each statement to its source and review. A context-only reference supports the record generally; it does not verify an individual field. Source checking does not reproduce an experiment.

One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.

38 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-10-09-9307685239b3
Property and statement	Original source and location	Review and provenance
attributes.comparison.adaptation Not reported Context-only references	Benchmarking of germline copy number variant callers from whole genome sequencing data for clinical applications Original source ↗ Supplemental Table 3, row 6 'Dragen v4.2 HS + Filters' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Bioinformatics Advances 5(1):vbaf071, published 2025-04-10; PMC12005901 full-text XML Retrieved: 2026-10-09T15:24:22Z	missing or unspecified No individual claim review recorded author reported Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.comparison.adaptation` Source artifact SHA-256: `ed6492f89d77454416d4fb135bb56bdcd5fb202e8a0ba94b92fa450441b4091f` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.adaptation Not reported Context-only references	De La Vega et al. 2025, Supplemental Table 3 Original source ↗ Supplemental Table 3, row 6 'Dragen v4.2 HS + Filters' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Supplemental_Table_3.xlsx inside vbaf071_supplementary_data.zip Retrieved: 2026-10-09T15:24:22Z	missing or unspecified No individual claim review recorded author reported Audit details Field: `attributes.comparison.adaptation` Source artifact SHA-256: `d900a69ec00915f1eb62dcf6b1ece0240cd4ba7937000652a6423fb813420bde` Hash scope: artifact_sha256 is the inner supplementary file. Containers: europepmc_supplementary_zip 52ad070b6703eb204924cb099e6bcbcdce0a4946235d3ef1c7c290469017584f; vbaf071_supplementary_data.zip 82318e5f18b797a277241a1b206a9aadd1e856cf4293eb79729185d314029691. The Europe PMC zip is rebuilt per request, so its hash describes one retrieval only. Inspected artifact
attributes.comparison.aggregation Single sample, per stratum Context-only references	Benchmarking of germline copy number variant callers from whole genome sequencing data for clinical applications Original source ↗ Supplemental Table 3, row 6 'Dragen v4.2 HS + Filters' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Bioinformatics Advances 5(1):vbaf071, published 2025-04-10; PMC12005901 full-text XML Retrieved: 2026-10-09T15:24:22Z	not individually reviewed No individual claim review recorded author reported Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.comparison.aggregation` Source artifact SHA-256: `ed6492f89d77454416d4fb135bb56bdcd5fb202e8a0ba94b92fa450441b4091f` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.aggregation Single sample, per stratum Context-only references	De La Vega et al. 2025, Supplemental Table 3 Original source ↗ Supplemental Table 3, row 6 'Dragen v4.2 HS + Filters' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Supplemental_Table_3.xlsx inside vbaf071_supplementary_data.zip Retrieved: 2026-10-09T15:24:22Z	not individually reviewed No individual claim review recorded author reported Audit details Field: `attributes.comparison.aggregation` Source artifact SHA-256: `d900a69ec00915f1eb62dcf6b1ece0240cd4ba7937000652a6423fb813420bde` Hash scope: artifact_sha256 is the inner supplementary file. Containers: europepmc_supplementary_zip 52ad070b6703eb204924cb099e6bcbcdce0a4946235d3ef1c7c290469017584f; vbaf071_supplementary_data.zip 82318e5f18b797a277241a1b206a9aadd1e856cf4293eb79729185d314029691. The Europe PMC zip is rebuilt per request, so its hash describes one retrieval only. Inspected artifact
attributes.comparison.budget Not reported Context-only references	Benchmarking of germline copy number variant callers from whole genome sequencing data for clinical applications Original source ↗ Supplemental Table 3, row 6 'Dragen v4.2 HS + Filters' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Bioinformatics Advances 5(1):vbaf071, published 2025-04-10; PMC12005901 full-text XML Retrieved: 2026-10-09T15:24:22Z	missing or unspecified No individual claim review recorded author reported Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.comparison.budget` Source artifact SHA-256: `ed6492f89d77454416d4fb135bb56bdcd5fb202e8a0ba94b92fa450441b4091f` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.budget Not reported Context-only references	De La Vega et al. 2025, Supplemental Table 3 Original source ↗ Supplemental Table 3, row 6 'Dragen v4.2 HS + Filters' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Supplemental_Table_3.xlsx inside vbaf071_supplementary_data.zip Retrieved: 2026-10-09T15:24:22Z	missing or unspecified No individual claim review recorded author reported Audit details Field: `attributes.comparison.budget` Source artifact SHA-256: `d900a69ec00915f1eb62dcf6b1ece0240cd4ba7937000652a6423fb813420bde` Hash scope: artifact_sha256 is the inner supplementary file. Containers: europepmc_supplementary_zip 52ad070b6703eb204924cb099e6bcbcdce0a4946235d3ef1c7c290469017584f; vbaf071_supplementary_data.zip 82318e5f18b797a277241a1b206a9aadd1e856cf4293eb79729185d314029691. The Europe PMC zip is rebuilt per request, so its hash describes one retrieval only. Inspected artifact
attributes.comparison.dataset_version GIAB HG002 SV v0.6 GRCh37 plus synthetic genes Context-only references	Benchmarking of germline copy number variant callers from whole genome sequencing data for clinical applications Original source ↗ Supplemental Table 3, row 6 'Dragen v4.2 HS + Filters' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Bioinformatics Advances 5(1):vbaf071, published 2025-04-10; PMC12005901 full-text XML Retrieved: 2026-10-09T15:24:22Z	not individually reviewed No individual claim review recorded author reported Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.comparison.dataset_version` Source artifact SHA-256: `ed6492f89d77454416d4fb135bb56bdcd5fb202e8a0ba94b92fa450441b4091f` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.dataset_version GIAB HG002 SV v0.6 GRCh37 plus synthetic genes Context-only references	De La Vega et al. 2025, Supplemental Table 3 Original source ↗ Supplemental Table 3, row 6 'Dragen v4.2 HS + Filters' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Supplemental_Table_3.xlsx inside vbaf071_supplementary_data.zip Retrieved: 2026-10-09T15:24:22Z	not individually reviewed No individual claim review recorded author reported Audit details Field: `attributes.comparison.dataset_version` Source artifact SHA-256: `d900a69ec00915f1eb62dcf6b1ece0240cd4ba7937000652a6423fb813420bde` Hash scope: artifact_sha256 is the inner supplementary file. Containers: europepmc_supplementary_zip 52ad070b6703eb204924cb099e6bcbcdce0a4946235d3ef1c7c290469017584f; vbaf071_supplementary_data.zip 82318e5f18b797a277241a1b206a9aadd1e856cf4293eb79729185d314029691. The Europe PMC zip is rebuilt per request, so its hash describes one retrieval only. Inspected artifact
attributes.comparison.inputs 50x PCR-free WGS, DRAGEN multi-genome BAM on GRCh37 Context-only references	Benchmarking of germline copy number variant callers from whole genome sequencing data for clinical applications Original source ↗ Supplemental Table 3, row 6 'Dragen v4.2 HS + Filters' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Bioinformatics Advances 5(1):vbaf071, published 2025-04-10; PMC12005901 full-text XML Retrieved: 2026-10-09T15:24:22Z	not individually reviewed No individual claim review recorded author reported Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.comparison.inputs` Source artifact SHA-256: `ed6492f89d77454416d4fb135bb56bdcd5fb202e8a0ba94b92fa450441b4091f` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.inputs 50x PCR-free WGS, DRAGEN multi-genome BAM on GRCh37 Context-only references	De La Vega et al. 2025, Supplemental Table 3 Original source ↗ Supplemental Table 3, row 6 'Dragen v4.2 HS + Filters' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Supplemental_Table_3.xlsx inside vbaf071_supplementary_data.zip Retrieved: 2026-10-09T15:24:22Z	not individually reviewed No individual claim review recorded author reported Audit details Field: `attributes.comparison.inputs` Source artifact SHA-256: `d900a69ec00915f1eb62dcf6b1ece0240cd4ba7937000652a6423fb813420bde` Hash scope: artifact_sha256 is the inner supplementary file. Containers: europepmc_supplementary_zip 52ad070b6703eb204924cb099e6bcbcdce0a4946235d3ef1c7c290469017584f; vbaf071_supplementary_data.zip 82318e5f18b797a277241a1b206a9aadd1e856cf4293eb79729185d314029691. The Europe PMC zip is rebuilt per request, so its hash describes one retrieval only. Inspected artifact

All evidence (JSONL) (gzip)How to read the evidence

Sources and history

Release 2026-10-09-9307685239b3 · Record review: source checked

2 source records and release history

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

Download this release (gzip)

Technical metadata and extraction receipts

Stable ID: cnv-20261009-eval-delavega2025-dragen42-hs-filters

areas: dna-genomes
contexts: clinical_research
origin: author_reported
protocol: cnv-20261009-protocol-delavega2025-hg002-exon-overlap
version: Primary source as retrieved 2026-10-09
comparison: protocol id: cnv-20261009-protocol-delavega2025-hg002-exon-overlap; dataset version: GIAB HG002 SV v0.6 GRCh37 plus synthetic genes; split: Single HG002 sample; population: 60 DEL and 10 DUP exon-overlapping truth events; inputs: 50x PCR-free WGS, DRAGEN multi-genome BAM on GRCh37; adaptation: Not reported; metric implementation: Not reported; aggregation: Single sample, per stratum; budget: Not reported
source locator: Supplemental Table 3, row 6 'Dragen v4.2 HS + Filters'
missing metadata: denominator: reason: unreported; note: Per-stratum counts unreported; metric implementation: reason: unreported; note: Evaluation code not identified
limitations: DRAGEN developer (Illumina) employees are co-authors; recorded as author_reported

Related records

system: DRAGEN 4.2 high-sensitivity mode with custom artifact filters (HS-F)
assessment: HG002 exon-overlap CNV benchmark by event type and length (De La Vega et al. Table S3)
data: HG002 50x PCR-free WGS with GIAB SV v0.6 CNV truth and synthetic gene models
evaluation: delavega2025-dragen42-hs-filters precision (deletions, 1-5 kb)
evaluation: delavega2025-dragen42-hs-filters precision (duplications, 1-5 kb)
evaluation: delavega2025-dragen42-hs-filters precision (deletions, 5-10 kb)
evaluation: delavega2025-dragen42-hs-filters precision (duplications, 5-10 kb)
evaluation: delavega2025-dragen42-hs-filters precision (deletions, 10-50 kb)
evaluation: delavega2025-dragen42-hs-filters precision (duplications, 10-50 kb)
evaluation: delavega2025-dragen42-hs-filters precision (deletions, 50 kb and over)
evaluation: delavega2025-dragen42-hs-filters precision (duplications, 50 kb and over)
evaluation: delavega2025-dragen42-hs-filters precision (deletions, all sizes)
evaluation: delavega2025-dragen42-hs-filters precision (duplications, all sizes)
evaluation: delavega2025-dragen42-hs-filters precision (deletions and duplications combined)
evaluation: delavega2025-dragen42-hs-filters recall (deletions, 1-5 kb)
evaluation: delavega2025-dragen42-hs-filters recall (duplications, 1-5 kb)
evaluation: delavega2025-dragen42-hs-filters recall (deletions, 5-10 kb)
evaluation: delavega2025-dragen42-hs-filters recall (duplications, 5-10 kb)
evaluation: delavega2025-dragen42-hs-filters recall (deletions, 10-50 kb)
evaluation: delavega2025-dragen42-hs-filters recall (duplications, 10-50 kb)
evaluation: delavega2025-dragen42-hs-filters recall (deletions, 50 kb and over)
evaluation: delavega2025-dragen42-hs-filters recall (duplications, 50 kb and over)
evaluation: delavega2025-dragen42-hs-filters recall (deletions, all sizes)
evaluation: delavega2025-dragen42-hs-filters recall (duplications, all sizes)
evaluation: delavega2025-dragen42-hs-filters recall (deletions and duplications combined)

Suggest a correction