Protocol

Exon-level CNV detection in clinical exomes against CMA truth, default calls (Hwang et al. Table 4, pre-filter)

Call CNVs with each tool on the 39 CMA-positive exomes; count CMA CNV exons detected (TP), missed (FN) and called exons outside the reference (FP); report sensitivity and PPV.

4 evaluations · 24 results

Overview

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4 recorded evaluations, 24 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

4 evaluations · 24 results. Different protocols are not a single leaderboard.

Protocol: Exon-level CNV detection in clinical exomes against CMA truth, default calls (Hwang et al. Table 4, pre-filter) · Dataset: Korea University clinical exomes with CMA reference CNVs (Hwang et al. 2026)

Sorted by False negatives (exon level) (lower is better). The best value in each column is highlighted. Decimals are rounded for display; each value links to the printed value and its source.

Tested configuration	False negatives (exon level)	False positives (exon level)	Precision (exon level)	Recall (exon level)	True positives (exon level)	Count (exon level; reference CMA CNV exons in the evaluated set)
CoNIFER v0.2.2, pre-filter (Hwang et al. 2026)Evaluation	646 (best in column)	6838 (best in column)	0.239 (best in column)	0.768 (best in column)	2142 (best in column)	2788
ExomeDepth v1.1.15, pre-filter (Hwang et al. 2026)Evaluation	674	83,135	0.025	0.758	2114	2788
CNVkit v0.9.7, pre-filter (Hwang et al. 2026)Evaluation	941	17,340	0.096	0.662	1847	2788
cn.MOPS v1.14.1, pre-filter (Hwang et al. 2026)Evaluation	2314	11,164	0.041	0.17	474	2788

All 24 result rows with coverage, uncertainty and sources

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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: cn.MOPS v1.14.1, pre-filter (Hwang et al. 2026)	Protocol: Exon-level CNV detection in clinical exomes against CMA truth, default calls (Hwang et al. Table 4, pre-filter) Dataset: Korea University clinical exomes with CMA reference CNVs (Hwang et al. 2026)	2310 False negatives (exon level) count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source cn.MOPS (pre-filter) on 39 clinical exomes against CMA truth cnv-20261011-hwang2026-protocol-pre-filter Aggregation: Not reported Improving CNV Detection Performance Except for Software-Specific Problematic Regions (Hwang et al., Genes 2026) · Table 4, row 'FN', column 'cn.MOPS' / 'Pre-filter'
Configuration: cn.MOPS v1.14.1, pre-filter (Hwang et al. 2026)	Protocol: Exon-level CNV detection in clinical exomes against CMA truth, default calls (Hwang et al. Table 4, pre-filter) Dataset: Korea University clinical exomes with CMA reference CNVs (Hwang et al. 2026)	11,164 False positives (exon level) count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source cn.MOPS (pre-filter) on 39 clinical exomes against CMA truth cnv-20261011-hwang2026-protocol-pre-filter Aggregation: Not reported Improving CNV Detection Performance Except for Software-Specific Problematic Regions (Hwang et al., Genes 2026) · Table 4, row 'FP', column 'cn.MOPS' / 'Pre-filter'
Configuration: cn.MOPS v1.14.1, pre-filter (Hwang et al. 2026)	Protocol: Exon-level CNV detection in clinical exomes against CMA truth, default calls (Hwang et al. Table 4, pre-filter) Dataset: Korea University clinical exomes with CMA reference CNVs (Hwang et al. 2026)	0.041 Precision (exon level) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source cn.MOPS (pre-filter) on 39 clinical exomes against CMA truth cnv-20261011-hwang2026-protocol-pre-filter Aggregation: Not reported Improving CNV Detection Performance Except for Software-Specific Problematic Regions (Hwang et al., Genes 2026) · Table 4, row 'PPV', column 'cn.MOPS' / 'Pre-filter'
Configuration: cn.MOPS v1.14.1, pre-filter (Hwang et al. 2026)	Protocol: Exon-level CNV detection in clinical exomes against CMA truth, default calls (Hwang et al. Table 4, pre-filter) Dataset: Korea University clinical exomes with CMA reference CNVs (Hwang et al. 2026)	2790 Count (exon level; reference CMA CNV exons in the evaluated set) count · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source cn.MOPS (pre-filter) on 39 clinical exomes against CMA truth cnv-20261011-hwang2026-protocol-pre-filter Aggregation: Not reported Improving CNV Detection Performance Except for Software-Specific Problematic Regions (Hwang et al., Genes 2026) · Table 4, row 'Reference Truth set', column 'cn.MOPS' / 'Pre-filter'
Configuration: cn.MOPS v1.14.1, pre-filter (Hwang et al. 2026)	Protocol: Exon-level CNV detection in clinical exomes against CMA truth, default calls (Hwang et al. Table 4, pre-filter) Dataset: Korea University clinical exomes with CMA reference CNVs (Hwang et al. 2026)	0.17 Recall (exon level) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source cn.MOPS (pre-filter) on 39 clinical exomes against CMA truth cnv-20261011-hwang2026-protocol-pre-filter Aggregation: Not reported Improving CNV Detection Performance Except for Software-Specific Problematic Regions (Hwang et al., Genes 2026) · Table 4, row 'Sensitivity', column 'cn.MOPS' / 'Pre-filter'
Configuration: cn.MOPS v1.14.1, pre-filter (Hwang et al. 2026)	Protocol: Exon-level CNV detection in clinical exomes against CMA truth, default calls (Hwang et al. Table 4, pre-filter) Dataset: Korea University clinical exomes with CMA reference CNVs (Hwang et al. 2026)	474 True positives (exon level) count · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source cn.MOPS (pre-filter) on 39 clinical exomes against CMA truth cnv-20261011-hwang2026-protocol-pre-filter Aggregation: Not reported Improving CNV Detection Performance Except for Software-Specific Problematic Regions (Hwang et al., Genes 2026) · Table 4, row 'TP', column 'cn.MOPS' / 'Pre-filter'
Configuration: CNVkit v0.9.7, pre-filter (Hwang et al. 2026)	Protocol: Exon-level CNV detection in clinical exomes against CMA truth, default calls (Hwang et al. Table 4, pre-filter) Dataset: Korea University clinical exomes with CMA reference CNVs (Hwang et al. 2026)	941 False negatives (exon level) count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source CNVkit (pre-filter) on 39 clinical exomes against CMA truth cnv-20261011-hwang2026-protocol-pre-filter Aggregation: Not reported Improving CNV Detection Performance Except for Software-Specific Problematic Regions (Hwang et al., Genes 2026) · Table 4, row 'FN', column 'CNVkit' / 'Pre-filter'
Configuration: CNVkit v0.9.7, pre-filter (Hwang et al. 2026)	Protocol: Exon-level CNV detection in clinical exomes against CMA truth, default calls (Hwang et al. Table 4, pre-filter) Dataset: Korea University clinical exomes with CMA reference CNVs (Hwang et al. 2026)	17,340 False positives (exon level) count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source CNVkit (pre-filter) on 39 clinical exomes against CMA truth cnv-20261011-hwang2026-protocol-pre-filter Aggregation: Not reported Improving CNV Detection Performance Except for Software-Specific Problematic Regions (Hwang et al., Genes 2026) · Table 4, row 'FP', column 'CNVkit' / 'Pre-filter'
Configuration: CNVkit v0.9.7, pre-filter (Hwang et al. 2026)	Protocol: Exon-level CNV detection in clinical exomes against CMA truth, default calls (Hwang et al. Table 4, pre-filter) Dataset: Korea University clinical exomes with CMA reference CNVs (Hwang et al. 2026)	0.096 Precision (exon level) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source CNVkit (pre-filter) on 39 clinical exomes against CMA truth cnv-20261011-hwang2026-protocol-pre-filter Aggregation: Not reported Improving CNV Detection Performance Except for Software-Specific Problematic Regions (Hwang et al., Genes 2026) · Table 4, row 'PPV', column 'CNVkit' / 'Pre-filter'
Configuration: CNVkit v0.9.7, pre-filter (Hwang et al. 2026)	Protocol: Exon-level CNV detection in clinical exomes against CMA truth, default calls (Hwang et al. Table 4, pre-filter) Dataset: Korea University clinical exomes with CMA reference CNVs (Hwang et al. 2026)	2790 Count (exon level; reference CMA CNV exons in the evaluated set) count · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source CNVkit (pre-filter) on 39 clinical exomes against CMA truth cnv-20261011-hwang2026-protocol-pre-filter Aggregation: Not reported Improving CNV Detection Performance Except for Software-Specific Problematic Regions (Hwang et al., Genes 2026) · Table 4, row 'Reference Truth set', column 'CNVkit' / 'Pre-filter'
Configuration: CNVkit v0.9.7, pre-filter (Hwang et al. 2026)	Protocol: Exon-level CNV detection in clinical exomes against CMA truth, default calls (Hwang et al. Table 4, pre-filter) Dataset: Korea University clinical exomes with CMA reference CNVs (Hwang et al. 2026)	0.662 Recall (exon level) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source CNVkit (pre-filter) on 39 clinical exomes against CMA truth cnv-20261011-hwang2026-protocol-pre-filter Aggregation: Not reported Improving CNV Detection Performance Except for Software-Specific Problematic Regions (Hwang et al., Genes 2026) · Table 4, row 'Sensitivity', column 'CNVkit' / 'Pre-filter'
Configuration: CNVkit v0.9.7, pre-filter (Hwang et al. 2026)	Protocol: Exon-level CNV detection in clinical exomes against CMA truth, default calls (Hwang et al. Table 4, pre-filter) Dataset: Korea University clinical exomes with CMA reference CNVs (Hwang et al. 2026)	1850 True positives (exon level) count · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source CNVkit (pre-filter) on 39 clinical exomes against CMA truth cnv-20261011-hwang2026-protocol-pre-filter Aggregation: Not reported Improving CNV Detection Performance Except for Software-Specific Problematic Regions (Hwang et al., Genes 2026) · Table 4, row 'TP', column 'CNVkit' / 'Pre-filter'
Configuration: CoNIFER v0.2.2, pre-filter (Hwang et al. 2026)	Protocol: Exon-level CNV detection in clinical exomes against CMA truth, default calls (Hwang et al. Table 4, pre-filter) Dataset: Korea University clinical exomes with CMA reference CNVs (Hwang et al. 2026)	646 False negatives (exon level) count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source CoNIFER (pre-filter) on 39 clinical exomes against CMA truth cnv-20261011-hwang2026-protocol-pre-filter Aggregation: Not reported Improving CNV Detection Performance Except for Software-Specific Problematic Regions (Hwang et al., Genes 2026) · Table 4, row 'FN', column 'CoNIFER' / 'Pre-filter'
Configuration: CoNIFER v0.2.2, pre-filter (Hwang et al. 2026)	Protocol: Exon-level CNV detection in clinical exomes against CMA truth, default calls (Hwang et al. Table 4, pre-filter) Dataset: Korea University clinical exomes with CMA reference CNVs (Hwang et al. 2026)	6840 False positives (exon level) count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source CoNIFER (pre-filter) on 39 clinical exomes against CMA truth cnv-20261011-hwang2026-protocol-pre-filter Aggregation: Not reported Improving CNV Detection Performance Except for Software-Specific Problematic Regions (Hwang et al., Genes 2026) · Table 4, row 'FP', column 'CoNIFER' / 'Pre-filter'
Configuration: CoNIFER v0.2.2, pre-filter (Hwang et al. 2026)	Protocol: Exon-level CNV detection in clinical exomes against CMA truth, default calls (Hwang et al. Table 4, pre-filter) Dataset: Korea University clinical exomes with CMA reference CNVs (Hwang et al. 2026)	0.239 Precision (exon level) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source CoNIFER (pre-filter) on 39 clinical exomes against CMA truth cnv-20261011-hwang2026-protocol-pre-filter Aggregation: Not reported Improving CNV Detection Performance Except for Software-Specific Problematic Regions (Hwang et al., Genes 2026) · Table 4, row 'PPV', column 'CoNIFER' / 'Pre-filter'
Configuration: CoNIFER v0.2.2, pre-filter (Hwang et al. 2026)	Protocol: Exon-level CNV detection in clinical exomes against CMA truth, default calls (Hwang et al. Table 4, pre-filter) Dataset: Korea University clinical exomes with CMA reference CNVs (Hwang et al. 2026)	2790 Count (exon level; reference CMA CNV exons in the evaluated set) count · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source CoNIFER (pre-filter) on 39 clinical exomes against CMA truth cnv-20261011-hwang2026-protocol-pre-filter Aggregation: Not reported Improving CNV Detection Performance Except for Software-Specific Problematic Regions (Hwang et al., Genes 2026) · Table 4, row 'Reference Truth set', column 'CoNIFER' / 'Pre-filter'
Configuration: CoNIFER v0.2.2, pre-filter (Hwang et al. 2026)	Protocol: Exon-level CNV detection in clinical exomes against CMA truth, default calls (Hwang et al. Table 4, pre-filter) Dataset: Korea University clinical exomes with CMA reference CNVs (Hwang et al. 2026)	0.768 Recall (exon level) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source CoNIFER (pre-filter) on 39 clinical exomes against CMA truth cnv-20261011-hwang2026-protocol-pre-filter Aggregation: Not reported Improving CNV Detection Performance Except for Software-Specific Problematic Regions (Hwang et al., Genes 2026) · Table 4, row 'Sensitivity', column 'CoNIFER' / 'Pre-filter'
Configuration: CoNIFER v0.2.2, pre-filter (Hwang et al. 2026)	Protocol: Exon-level CNV detection in clinical exomes against CMA truth, default calls (Hwang et al. Table 4, pre-filter) Dataset: Korea University clinical exomes with CMA reference CNVs (Hwang et al. 2026)	2140 True positives (exon level) count · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source CoNIFER (pre-filter) on 39 clinical exomes against CMA truth cnv-20261011-hwang2026-protocol-pre-filter Aggregation: Not reported Improving CNV Detection Performance Except for Software-Specific Problematic Regions (Hwang et al., Genes 2026) · Table 4, row 'TP', column 'CoNIFER' / 'Pre-filter'
Configuration: ExomeDepth v1.1.15, pre-filter (Hwang et al. 2026)	Protocol: Exon-level CNV detection in clinical exomes against CMA truth, default calls (Hwang et al. Table 4, pre-filter) Dataset: Korea University clinical exomes with CMA reference CNVs (Hwang et al. 2026)	674 False negatives (exon level) count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source ExomeDepth (pre-filter) on 39 clinical exomes against CMA truth cnv-20261011-hwang2026-protocol-pre-filter Aggregation: Not reported Improving CNV Detection Performance Except for Software-Specific Problematic Regions (Hwang et al., Genes 2026) · Table 4, row 'FN', column 'ExomeDepth' / 'Pre-filter'
Configuration: ExomeDepth v1.1.15, pre-filter (Hwang et al. 2026)	Protocol: Exon-level CNV detection in clinical exomes against CMA truth, default calls (Hwang et al. Table 4, pre-filter) Dataset: Korea University clinical exomes with CMA reference CNVs (Hwang et al. 2026)	83,135 False positives (exon level) count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source ExomeDepth (pre-filter) on 39 clinical exomes against CMA truth cnv-20261011-hwang2026-protocol-pre-filter Aggregation: Not reported Improving CNV Detection Performance Except for Software-Specific Problematic Regions (Hwang et al., Genes 2026) · Table 4, row 'FP', column 'ExomeDepth' / 'Pre-filter'
Configuration: ExomeDepth v1.1.15, pre-filter (Hwang et al. 2026)	Protocol: Exon-level CNV detection in clinical exomes against CMA truth, default calls (Hwang et al. Table 4, pre-filter) Dataset: Korea University clinical exomes with CMA reference CNVs (Hwang et al. 2026)	0.025 Precision (exon level) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source ExomeDepth (pre-filter) on 39 clinical exomes against CMA truth cnv-20261011-hwang2026-protocol-pre-filter Aggregation: Not reported Improving CNV Detection Performance Except for Software-Specific Problematic Regions (Hwang et al., Genes 2026) · Table 4, row 'PPV', column 'ExomeDepth' / 'Pre-filter'
Configuration: ExomeDepth v1.1.15, pre-filter (Hwang et al. 2026)	Protocol: Exon-level CNV detection in clinical exomes against CMA truth, default calls (Hwang et al. Table 4, pre-filter) Dataset: Korea University clinical exomes with CMA reference CNVs (Hwang et al. 2026)	2790 Count (exon level; reference CMA CNV exons in the evaluated set) count · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source ExomeDepth (pre-filter) on 39 clinical exomes against CMA truth cnv-20261011-hwang2026-protocol-pre-filter Aggregation: Not reported Improving CNV Detection Performance Except for Software-Specific Problematic Regions (Hwang et al., Genes 2026) · Table 4, row 'Reference Truth set', column 'ExomeDepth' / 'Pre-filter'
Configuration: ExomeDepth v1.1.15, pre-filter (Hwang et al. 2026)	Protocol: Exon-level CNV detection in clinical exomes against CMA truth, default calls (Hwang et al. Table 4, pre-filter) Dataset: Korea University clinical exomes with CMA reference CNVs (Hwang et al. 2026)	0.758 Recall (exon level) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source ExomeDepth (pre-filter) on 39 clinical exomes against CMA truth cnv-20261011-hwang2026-protocol-pre-filter Aggregation: Not reported Improving CNV Detection Performance Except for Software-Specific Problematic Regions (Hwang et al., Genes 2026) · Table 4, row 'Sensitivity', column 'ExomeDepth' / 'Pre-filter'
Configuration: ExomeDepth v1.1.15, pre-filter (Hwang et al. 2026)	Protocol: Exon-level CNV detection in clinical exomes against CMA truth, default calls (Hwang et al. Table 4, pre-filter) Dataset: Korea University clinical exomes with CMA reference CNVs (Hwang et al. 2026)	2110 True positives (exon level) count · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source ExomeDepth (pre-filter) on 39 clinical exomes against CMA truth cnv-20261011-hwang2026-protocol-pre-filter Aggregation: Not reported Improving CNV Detection Performance Except for Software-Specific Problematic Regions (Hwang et al., Genes 2026) · Table 4, row 'TP', column 'ExomeDepth' / 'Pre-filter'

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Improving CNV Detection Performance Except for Software-Specific Problematic Regions (Hwang et al., Genes 2026) · Original source · Genes 17(1):105, published 2026-01-19; PMC12841491 full-text XML

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Technical metadata and extraction receipts

Stable ID: cnv-20261011-hwang2026-protocol-pre-filter

areas: dna-genomes
contexts: clinical_research
protocol: Call CNVs with each tool on the 39 CMA-positive exomes; count CMA CNV exons detected (TP), missed (FN) and called exons outside the reference (FP); report sensitivity and PPV.
version: Table 4
source locator: Table 4; Methods 2.2, 2.4 and 2.5; Results 3.3
limitations: Exome input, not the whole-genome input this use case names.; Exon-level scoring against CMA-derived truth: CMA misses small CNVs and only CNVs overlapping exome baits were kept, so precision counts any exon call outside that truth as false.; 39 individuals from one centre; no uncertainty intervals are printed.

Related records

uses data: Korea University clinical exomes with CMA reference CNVs (Hwang et al. 2026)
assessment: cn.MOPS (pre-filter) on 39 clinical exomes against CMA truth
assessment: CNVkit (pre-filter) on 39 clinical exomes against CMA truth
assessment: CoNIFER (pre-filter) on 39 clinical exomes against CMA truth
assessment: ExomeDepth (pre-filter) on 39 clinical exomes against CMA truth
assessed by: Select a copy-number variant detection and characterisation workflow

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