Protocol

NA12878 WGS CNV recall and precision, 1 bp overlap (Gabrielaite et al. Table S2)

Per-tool CNV calls on NA12878 WGS compared with the gold-standard CNV set.

Overview

Per-tool CNV calls on NA12878 WGS compared with the gold-standard CNV set.

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

8 recorded evaluations, 16 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

8 evaluations · 16 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: CLC Genomics Workbench (Gabrielaite et al. WGS)	Protocol: NA12878 WGS CNV recall and precision, 1 bp overlap (Gabrielaite et al. Table S2) Dataset: NA12878 WGS with the Haraksingh et al. 2017 gold-standard CNV set	0.667 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 CLC Genomics Workbench on NA12878 WGS cnv-20261009-protocol-gabrielaite2021-na12878-wgs-overlap Aggregation: Not reported A Comparison of Tools for Copy-Number Variation Detection in Germline Whole Exome and Whole Genome Sequencing Data; Gabrielaite et al. 2021, Table S2 (precision and recall of CNV calling tools) · Table S2.xlsx, sheet Supplementary_table2, K40; sample GB-WGS-NA12878; tool CLC; column precision
Configuration: CLC Genomics Workbench (Gabrielaite et al. WGS)	Protocol: NA12878 WGS CNV recall and precision, 1 bp overlap (Gabrielaite et al. Table S2) Dataset: NA12878 WGS with the Haraksingh et al. 2017 gold-standard CNV set	0.0116 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 CLC Genomics Workbench on NA12878 WGS cnv-20261009-protocol-gabrielaite2021-na12878-wgs-overlap Aggregation: Not reported A Comparison of Tools for Copy-Number Variation Detection in Germline Whole Exome and Whole Genome Sequencing Data; Gabrielaite et al. 2021, Table S2 (precision and recall of CNV calling tools) · Table S2.xlsx, sheet Supplementary_table2, L40; sample GB-WGS-NA12878; tool CLC; column recall
Configuration: cn.MOPS (Gabrielaite et al. WGS)	Protocol: NA12878 WGS CNV recall and precision, 1 bp overlap (Gabrielaite et al. Table S2) Dataset: NA12878 WGS with the Haraksingh et al. 2017 gold-standard CNV set	0.123 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 cn.MOPS on NA12878 WGS cnv-20261009-protocol-gabrielaite2021-na12878-wgs-overlap Aggregation: Not reported A Comparison of Tools for Copy-Number Variation Detection in Germline Whole Exome and Whole Genome Sequencing Data; Gabrielaite et al. 2021, Table S2 (precision and recall of CNV calling tools) · Table S2.xlsx, sheet Supplementary_table2, K88; sample GB-WGS-NA12878; tool cn.MOPS; column precision
Configuration: cn.MOPS (Gabrielaite et al. WGS)	Protocol: NA12878 WGS CNV recall and precision, 1 bp overlap (Gabrielaite et al. Table S2) Dataset: NA12878 WGS with the Haraksingh et al. 2017 gold-standard CNV set	0.17 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 cn.MOPS on NA12878 WGS cnv-20261009-protocol-gabrielaite2021-na12878-wgs-overlap Aggregation: Not reported A Comparison of Tools for Copy-Number Variation Detection in Germline Whole Exome and Whole Genome Sequencing Data; Gabrielaite et al. 2021, Table S2 (precision and recall of CNV calling tools) · Table S2.xlsx, sheet Supplementary_table2, L88; sample GB-WGS-NA12878; tool cn.MOPS; column recall
Configuration: CNVnator (Gabrielaite et al. WGS)	Protocol: NA12878 WGS CNV recall and precision, 1 bp overlap (Gabrielaite et al. Table S2) Dataset: NA12878 WGS with the Haraksingh et al. 2017 gold-standard CNV set	0.128 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 on NA12878 WGS cnv-20261009-protocol-gabrielaite2021-na12878-wgs-overlap Aggregation: Not reported A Comparison of Tools for Copy-Number Variation Detection in Germline Whole Exome and Whole Genome Sequencing Data; Gabrielaite et al. 2021, Table S2 (precision and recall of CNV calling tools) · Table S2.xlsx, sheet Supplementary_table2, K136; sample GB-WGS-NA12878; tool CNVnator; column precision
Configuration: CNVnator (Gabrielaite et al. WGS)	Protocol: NA12878 WGS CNV recall and precision, 1 bp overlap (Gabrielaite et al. Table S2) Dataset: NA12878 WGS with the Haraksingh et al. 2017 gold-standard CNV set	0.434 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 on NA12878 WGS cnv-20261009-protocol-gabrielaite2021-na12878-wgs-overlap Aggregation: Not reported A Comparison of Tools for Copy-Number Variation Detection in Germline Whole Exome and Whole Genome Sequencing Data; Gabrielaite et al. 2021, Table S2 (precision and recall of CNV calling tools) · Table S2.xlsx, sheet Supplementary_table2, L136; sample GB-WGS-NA12878; tool CNVnator; column recall
Configuration: Control-FREEC (Gabrielaite et al. WGS)	Protocol: NA12878 WGS CNV recall and precision, 1 bp overlap (Gabrielaite et al. Table S2) Dataset: NA12878 WGS with the Haraksingh et al. 2017 gold-standard CNV set	0.267 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 Control-FREEC on NA12878 WGS cnv-20261009-protocol-gabrielaite2021-na12878-wgs-overlap Aggregation: Not reported A Comparison of Tools for Copy-Number Variation Detection in Germline Whole Exome and Whole Genome Sequencing Data; Gabrielaite et al. 2021, Table S2 (precision and recall of CNV calling tools) · Table S2.xlsx, sheet Supplementary_table2, K175; sample GB-WGS-NA12878; tool ControlFREEC; column precision
Configuration: Control-FREEC (Gabrielaite et al. WGS)	Protocol: NA12878 WGS CNV recall and precision, 1 bp overlap (Gabrielaite et al. Table S2) Dataset: NA12878 WGS with the Haraksingh et al. 2017 gold-standard CNV set	0.107 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 Control-FREEC on NA12878 WGS cnv-20261009-protocol-gabrielaite2021-na12878-wgs-overlap Aggregation: Not reported A Comparison of Tools for Copy-Number Variation Detection in Germline Whole Exome and Whole Genome Sequencing Data; Gabrielaite et al. 2021, Table S2 (precision and recall of CNV calling tools) · Table S2.xlsx, sheet Supplementary_table2, L175; sample GB-WGS-NA12878; tool ControlFREEC; column recall
Configuration: DELLY (Gabrielaite et al. WGS)	Protocol: NA12878 WGS CNV recall and precision, 1 bp overlap (Gabrielaite et al. Table S2) Dataset: NA12878 WGS with the Haraksingh et al. 2017 gold-standard CNV set	0.199 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 DELLY on NA12878 WGS cnv-20261009-protocol-gabrielaite2021-na12878-wgs-overlap Aggregation: Not reported A Comparison of Tools for Copy-Number Variation Detection in Germline Whole Exome and Whole Genome Sequencing Data; Gabrielaite et al. 2021, Table S2 (precision and recall of CNV calling tools) · Table S2.xlsx, sheet Supplementary_table2, K214; sample GB-WGS-NA12878; tool DELLY; column precision
Configuration: DELLY (Gabrielaite et al. WGS)	Protocol: NA12878 WGS CNV recall and precision, 1 bp overlap (Gabrielaite et al. Table S2) Dataset: NA12878 WGS with the Haraksingh et al. 2017 gold-standard CNV set	0.904 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 DELLY on NA12878 WGS cnv-20261009-protocol-gabrielaite2021-na12878-wgs-overlap Aggregation: Not reported A Comparison of Tools for Copy-Number Variation Detection in Germline Whole Exome and Whole Genome Sequencing Data; Gabrielaite et al. 2021, Table S2 (precision and recall of CNV calling tools) · Table S2.xlsx, sheet Supplementary_table2, L214; sample GB-WGS-NA12878; tool DELLY; column recall
Configuration: GATK gCNV (Gabrielaite et al. WGS)	Protocol: NA12878 WGS CNV recall and precision, 1 bp overlap (Gabrielaite et al. Table S2) Dataset: NA12878 WGS with the Haraksingh et al. 2017 gold-standard CNV set	0.0186 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 GATK gCNV on NA12878 WGS cnv-20261009-protocol-gabrielaite2021-na12878-wgs-overlap Aggregation: Not reported A Comparison of Tools for Copy-Number Variation Detection in Germline Whole Exome and Whole Genome Sequencing Data; Gabrielaite et al. 2021, Table S2 (precision and recall of CNV calling tools) · Table S2.xlsx, sheet Supplementary_table2, K292; sample GB-WGS-NA12878; tool GATK_gCNV; column precision
Configuration: GATK gCNV (Gabrielaite et al. WGS)	Protocol: NA12878 WGS CNV recall and precision, 1 bp overlap (Gabrielaite et al. Table S2) Dataset: NA12878 WGS with the Haraksingh et al. 2017 gold-standard CNV set	0.232 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 GATK gCNV on NA12878 WGS cnv-20261009-protocol-gabrielaite2021-na12878-wgs-overlap Aggregation: Not reported A Comparison of Tools for Copy-Number Variation Detection in Germline Whole Exome and Whole Genome Sequencing Data; Gabrielaite et al. 2021, Table S2 (precision and recall of CNV calling tools) · Table S2.xlsx, sheet Supplementary_table2, L292; sample GB-WGS-NA12878; tool GATK_gCNV; column recall
Configuration: LUMPY (lumpyexpress) (Gabrielaite et al. WGS)	Protocol: NA12878 WGS CNV recall and precision, 1 bp overlap (Gabrielaite et al. Table S2) Dataset: NA12878 WGS with the Haraksingh et al. 2017 gold-standard CNV set	0.31 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 LUMPY (lumpyexpress) on NA12878 WGS cnv-20261009-protocol-gabrielaite2021-na12878-wgs-overlap Aggregation: Not reported A Comparison of Tools for Copy-Number Variation Detection in Germline Whole Exome and Whole Genome Sequencing Data; Gabrielaite et al. 2021, Table S2 (precision and recall of CNV calling tools) · Table S2.xlsx, sheet Supplementary_table2, K253; sample GB-WGS-NA12878; tool Lumpy; column precision
Configuration: LUMPY (lumpyexpress) (Gabrielaite et al. WGS)	Protocol: NA12878 WGS CNV recall and precision, 1 bp overlap (Gabrielaite et al. Table S2) Dataset: NA12878 WGS with the Haraksingh et al. 2017 gold-standard CNV set	0.941 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 LUMPY (lumpyexpress) on NA12878 WGS cnv-20261009-protocol-gabrielaite2021-na12878-wgs-overlap Aggregation: Not reported A Comparison of Tools for Copy-Number Variation Detection in Germline Whole Exome and Whole Genome Sequencing Data; Gabrielaite et al. 2021, Table S2 (precision and recall of CNV calling tools) · Table S2.xlsx, sheet Supplementary_table2, L253; sample GB-WGS-NA12878; tool Lumpy; column recall
Configuration: Manta (Gabrielaite et al. WGS)	Protocol: NA12878 WGS CNV recall and precision, 1 bp overlap (Gabrielaite et al. Table S2) Dataset: NA12878 WGS with the Haraksingh et al. 2017 gold-standard CNV set	0.326 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 Manta on NA12878 WGS cnv-20261009-protocol-gabrielaite2021-na12878-wgs-overlap Aggregation: Not reported A Comparison of Tools for Copy-Number Variation Detection in Germline Whole Exome and Whole Genome Sequencing Data; Gabrielaite et al. 2021, Table S2 (precision and recall of CNV calling tools) · Table S2.xlsx, sheet Supplementary_table2, K340; sample GB-WGS-NA12878; tool Manta; column precision
Configuration: Manta (Gabrielaite et al. WGS)	Protocol: NA12878 WGS CNV recall and precision, 1 bp overlap (Gabrielaite et al. Table S2) Dataset: NA12878 WGS with the Haraksingh et al. 2017 gold-standard CNV set	0.875 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 Manta on NA12878 WGS cnv-20261009-protocol-gabrielaite2021-na12878-wgs-overlap Aggregation: Not reported A Comparison of Tools for Copy-Number Variation Detection in Germline Whole Exome and Whole Genome Sequencing Data; Gabrielaite et al. 2021, Table S2 (precision and recall of CNV calling tools) · Table S2.xlsx, sheet Supplementary_table2, L340; sample GB-WGS-NA12878; tool Manta; column recall

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External evaluations: 8

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2 source records and release history

A Comparison of Tools for Copy-Number Variation Detection in Germline Whole Exome and Whole Genome Sequencing Data · Original source · Cancers 13(24):6283, published 2021-12-14; PMC8699073 full-text XML
Gabrielaite et al. 2021, Table S2 (precision and recall of CNV calling tools) · Original source · Supplementary Materials/Table S2.xlsx inside cancers-13-06283-s001.zip

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Technical metadata and extraction receipts

Stable ID: cnv-20261009-protocol-gabrielaite2021-na12878-wgs-overlap

areas: dna-genomes
contexts: clinical_research
protocol: A call is a true positive if it overlaps a truth CNV by at least 1 bp; Recall = TP/(TP+FN), Precision = TP/(TP+FP). Default parameters; no confidence filtering except where the tool does it by default.
version: Table S2 rows with sample 'GB-WGS-NA12878'
limitations: Manta and CNVnator were used to build the NA12878 truth set, which can favour them (Results 3.7).; 1 bp overlap is a lenient match and ignores dosage direction in the stated formula.; Cohort rows GB-WGS-01 to 38 (SNP-array reference) and WES rows are not extracted in this pass.; Most tool versions unreported in the article
missing metadata: metric definition: reason: unreported; note: Whether DEL/DUP type must match is not stated

Related records

uses data: NA12878 WGS with the Haraksingh et al. 2017 gold-standard CNV set
assessment: CLC Genomics Workbench on NA12878 WGS
assessment: cn.MOPS on NA12878 WGS
assessment: CNVnator on NA12878 WGS
assessment: Control-FREEC on NA12878 WGS
assessment: DELLY on NA12878 WGS
assessment: GATK gCNV on NA12878 WGS
assessment: LUMPY (lumpyexpress) on NA12878 WGS
assessment: Manta on NA12878 WGS
assessed by: Select a copy-number variant detection and characterisation workflow

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