Protocol

HG002 GIAB v0.6 CNV deletion [20,000-50,000) bp (DRAGEN Table S4)

One length bin of the DRAGEN CNV benchmark.

Overview

One length bin of the DRAGEN CNV benchmark.

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

3 recorded evaluations, 9 metric rows. A comparison chart has not yet been validated for these results. The table retains the individual findings and their sources.

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Results

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All evaluations

3 evaluations · 9 results. Different protocols are not a single leaderboard.

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Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: CNVnator comparator (Behera et al. Table S4)	Protocol: HG002 GIAB v0.6 CNV deletion [20,000-50,000) bp (DRAGEN Table S4) Dataset: HG002 35x WGS, GIAB SV v0.6 deletions >1 kb, Table S4 length bins	0.949 f1-score fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source CNVnator deletion [20,000-50,000) cnv-20261009-protocol-behera2024-hg002-cnv-del-20-50kb Aggregation: Not reported Comprehensive genome analysis and variant detection at scale using DRAGEN; DRAGEN supplementary tables 1–17 · Supplementary Tables XLSX sheet 'S4 CNV benchmarking', L9; row [20,000-50,000); column CNVnator F-score
Configuration: CNVnator comparator (Behera et al. Table S4)	Protocol: HG002 GIAB v0.6 CNV deletion [20,000-50,000) bp (DRAGEN Table S4) Dataset: HG002 35x WGS, GIAB SV v0.6 deletions >1 kb, Table S4 length bins	0.984 precision fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source CNVnator deletion [20,000-50,000) cnv-20261009-protocol-behera2024-hg002-cnv-del-20-50kb Aggregation: Not reported Comprehensive genome analysis and variant detection at scale using DRAGEN; DRAGEN supplementary tables 1–17 · Supplementary Tables XLSX sheet 'S4 CNV benchmarking', K9; row [20,000-50,000); column CNVnator Precision
Configuration: CNVnator comparator (Behera et al. Table S4)	Protocol: HG002 GIAB v0.6 CNV deletion [20,000-50,000) bp (DRAGEN Table S4) Dataset: HG002 35x WGS, GIAB SV v0.6 deletions >1 kb, Table S4 length bins	0.916 recall fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source CNVnator deletion [20,000-50,000) cnv-20261009-protocol-behera2024-hg002-cnv-del-20-50kb Aggregation: Not reported Comprehensive genome analysis and variant detection at scale using DRAGEN; DRAGEN supplementary tables 1–17 · Supplementary Tables XLSX sheet 'S4 CNV benchmarking', J9; row [20,000-50,000); column CNVnator Recall
Configuration: DRAGEN 4.2 CNV-only configuration (Behera et al. Table S4)	Protocol: HG002 GIAB v0.6 CNV deletion [20,000-50,000) bp (DRAGEN Table S4) Dataset: HG002 35x WGS, GIAB SV v0.6 deletions >1 kb, Table S4 length bins	0.903 f1-score fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source DRAGEN4.2 (CNV) deletion [20,000-50,000) cnv-20261009-protocol-behera2024-hg002-cnv-del-20-50kb Aggregation: Not reported Comprehensive genome analysis and variant detection at scale using DRAGEN; DRAGEN supplementary tables 1–17 · Supplementary Tables XLSX sheet 'S4 CNV benchmarking', D9; row [20,000-50,000); column DRAGEN4.2 (CNV) F-score
Configuration: DRAGEN 4.2 CNV-only configuration (Behera et al. Table S4)	Protocol: HG002 GIAB v0.6 CNV deletion [20,000-50,000) bp (DRAGEN Table S4) Dataset: HG002 35x WGS, GIAB SV v0.6 deletions >1 kb, Table S4 length bins	0.967 precision fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source DRAGEN4.2 (CNV) deletion [20,000-50,000) cnv-20261009-protocol-behera2024-hg002-cnv-del-20-50kb Aggregation: Not reported Comprehensive genome analysis and variant detection at scale using DRAGEN; DRAGEN supplementary tables 1–17 · Supplementary Tables XLSX sheet 'S4 CNV benchmarking', C9; row [20,000-50,000); column DRAGEN4.2 (CNV) Precision
Configuration: DRAGEN 4.2 CNV-only configuration (Behera et al. Table S4)	Protocol: HG002 GIAB v0.6 CNV deletion [20,000-50,000) bp (DRAGEN Table S4) Dataset: HG002 35x WGS, GIAB SV v0.6 deletions >1 kb, Table S4 length bins	0.85 recall fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source DRAGEN4.2 (CNV) deletion [20,000-50,000) cnv-20261009-protocol-behera2024-hg002-cnv-del-20-50kb Aggregation: Not reported Comprehensive genome analysis and variant detection at scale using DRAGEN; DRAGEN supplementary tables 1–17 · Supplementary Tables XLSX sheet 'S4 CNV benchmarking', B9; row [20,000-50,000); column DRAGEN4.2 (CNV) Recall
Configuration: DRAGEN 4.2 CNV+SV configuration	Protocol: HG002 GIAB v0.6 CNV deletion [20,000-50,000) bp (DRAGEN Table S4) Dataset: HG002 35x WGS, GIAB SV v0.6 deletions >1 kb, Table S4 length bins	0.952 f1-score fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source DRAGEN4.2 (CNV+SV) deletion [20,000-50,000) cnv-20261009-protocol-behera2024-hg002-cnv-del-20-50kb Aggregation: Not reported Comprehensive genome analysis and variant detection at scale using DRAGEN; DRAGEN supplementary tables 1–17 · Supplementary Tables XLSX sheet 'S4 CNV benchmarking', H9; row [20,000-50,000); column DRAGEN4.2 (CNV+SV) F-score
Configuration: DRAGEN 4.2 CNV+SV configuration	Protocol: HG002 GIAB v0.6 CNV deletion [20,000-50,000) bp (DRAGEN Table S4) Dataset: HG002 35x WGS, GIAB SV v0.6 deletions >1 kb, Table S4 length bins	1 precision fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source DRAGEN4.2 (CNV+SV) deletion [20,000-50,000) cnv-20261009-protocol-behera2024-hg002-cnv-del-20-50kb Aggregation: Not reported Comprehensive genome analysis and variant detection at scale using DRAGEN; DRAGEN supplementary tables 1–17 · Supplementary Tables XLSX sheet 'S4 CNV benchmarking', G9; row [20,000-50,000); column DRAGEN4.2 (CNV+SV) Precision
Configuration: DRAGEN 4.2 CNV+SV configuration	Protocol: HG002 GIAB v0.6 CNV deletion [20,000-50,000) bp (DRAGEN Table S4) Dataset: HG002 35x WGS, GIAB SV v0.6 deletions >1 kb, Table S4 length bins	0.909 recall fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source DRAGEN4.2 (CNV+SV) deletion [20,000-50,000) cnv-20261009-protocol-behera2024-hg002-cnv-del-20-50kb Aggregation: Not reported Comprehensive genome analysis and variant detection at scale using DRAGEN; DRAGEN supplementary tables 1–17 · Supplementary Tables XLSX sheet 'S4 CNV benchmarking', F9; row [20,000-50,000); column DRAGEN4.2 (CNV+SV) Recall

Source checking is not independent reproduction. Release 2026-10-09-8eac2440869c.

Methods and evaluation design

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Baseline coverage

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Author-reported evaluations: 2
External evaluations: 1

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Strengths, limitations and unresolved questions

Evidence

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Evidence table

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Sources and history

Release 2026-10-09-8eac2440869c · Record review: source checked

2 source records and release history

Comprehensive genome analysis and variant detection at scale using DRAGEN · Original source · 2024-10-25 version of record; code-availability correction 2024-12-02; July 2025 issue
DRAGEN supplementary tables 1–17 · Original source · MOESM3 XLSX retrieved 2026-10-07

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Technical metadata and extraction receipts

Stable ID: cnv-20261009-protocol-behera2024-hg002-cnv-del-20-50kb

areas: dna-genomes
contexts: clinical_research
protocol: Compare copy-number calls to >1 kb deletion records in GIAB SV v0.6; length bin printed as [20,000-50,000).
version: Table S4 row 9
limitations: Deletions in one reference sample only; no duplication, tumour or clinical endpoint.; CNVnator values in Table S4 and in the article prose differ for the 1-5 kb bin (AMP intake); prose not re-read here.
missing metadata: denominator: reason: unreported; note: Per-bin counts unreported; metric implementation: reason: unextracted; note: Exact CNV matching implementation unextracted

Related records

uses data: HG002 35x WGS, GIAB SV v0.6 deletions >1 kb, Table S4 length bins
assessment: CNVnator deletion [20,000-50,000)
assessment: DRAGEN4.2 (CNV) deletion [20,000-50,000)
assessment: DRAGEN4.2 (CNV+SV) deletion [20,000-50,000)
assessed by: Select a copy-number variant detection and characterisation workflow

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