Gold-standard sample in the Gabrielaite et al. benchmark.
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Release 2026-10-09-9307685239b3 · Evidence verified: Not verified
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8 evaluations · 16 results. Different protocols are not a single leaderboard.
Applied filters: All linked evaluations
| 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 checkedMethods, coverage and sourceCLC 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 checkedMethods, coverage and sourceCLC 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 checkedMethods, coverage and sourcecnv-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 checkedMethods, coverage and sourcecnv-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 checkedMethods, coverage and sourcecnv-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 checkedMethods, coverage and sourcecnv-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 checkedMethods, coverage and sourcecnv-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 checkedMethods, coverage and sourcecnv-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 checkedMethods, coverage and sourcecnv-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 checkedMethods, coverage and sourcecnv-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 checkedMethods, coverage and sourcecnv-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 checkedMethods, coverage and sourcecnv-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 checkedMethods, coverage and sourceLUMPY (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 checkedMethods, coverage and sourceLUMPY (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 checkedMethods, coverage and sourcecnv-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 checkedMethods, coverage and sourcecnv-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 |
Source checking is not independent reproduction. Release 2026-10-09-9307685239b3.
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One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.
12 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| attributes.population NA12878 WGS, Nextera DNA Flex, NovaSeq 6000, >=30x, 150 bp reads, BWA-MEM 0.7.12 to hg19/GRCh37. Context-only references | A Comparison of Tools for Copy-Number Variation Detection in Germline Whole Exome and Whole Genome Sequencing Data Methods 2.1 and 2.5; Table S2 rows 'GB-WGS-NA12878' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Cancers 13(24):6283, published 2021-12-14; PMC8699073 full-text XML | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.population NA12878 WGS, Nextera DNA Flex, NovaSeq 6000, >=30x, 150 bp reads, BWA-MEM 0.7.12 to hg19/GRCh37. Context-only references | Gabrielaite et al. 2021, Table S2 (precision and recall of CNV calling tools) Methods 2.1 and 2.5; Table S2 rows 'GB-WGS-NA12878' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Supplementary Materials/Table S2.xlsx inside cancers-13-06283-s001.zip | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: artifact_sha256 is the inner supplementary file. Containers: europepmc_supplementary_zip 3ecf626259edf3ee82a10b76a20be078382d4e7ecb4b4fa5145143c4d5ccbf51; cancers-13-06283-s001.zip 0fd70ccaf67605cfa4a05a6f65666bfa16812c75ac53f865860b6e8e7eb9deac. The Europe PMC zip is rebuilt per request, so its hash describes one retrieval only. |
| attributes.source_locator Methods 2.1 and 2.5; Table S2 rows 'GB-WGS-NA12878' Context-only references | A Comparison of Tools for Copy-Number Variation Detection in Germline Whole Exome and Whole Genome Sequencing Data Methods 2.1 and 2.5; Table S2 rows 'GB-WGS-NA12878' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Cancers 13(24):6283, published 2021-12-14; PMC8699073 full-text XML | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.source_locator Methods 2.1 and 2.5; Table S2 rows 'GB-WGS-NA12878' Context-only references | Gabrielaite et al. 2021, Table S2 (precision and recall of CNV calling tools) Methods 2.1 and 2.5; Table S2 rows 'GB-WGS-NA12878' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Supplementary Materials/Table S2.xlsx inside cancers-13-06283-s001.zip | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: artifact_sha256 is the inner supplementary file. Containers: europepmc_supplementary_zip 3ecf626259edf3ee82a10b76a20be078382d4e7ecb4b4fa5145143c4d5ccbf51; cancers-13-06283-s001.zip 0fd70ccaf67605cfa4a05a6f65666bfa16812c75ac53f865860b6e8e7eb9deac. The Europe PMC zip is rebuilt per request, so its hash describes one retrieval only. |
| attributes.split Single sample (NA12878, sequenced in house) Context-only references | A Comparison of Tools for Copy-Number Variation Detection in Germline Whole Exome and Whole Genome Sequencing Data Methods 2.1 and 2.5; Table S2 rows 'GB-WGS-NA12878' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Cancers 13(24):6283, published 2021-12-14; PMC8699073 full-text XML | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.split Single sample (NA12878, sequenced in house) Context-only references | Gabrielaite et al. 2021, Table S2 (precision and recall of CNV calling tools) Methods 2.1 and 2.5; Table S2 rows 'GB-WGS-NA12878' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Supplementary Materials/Table S2.xlsx inside cancers-13-06283-s001.zip | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: artifact_sha256 is the inner supplementary file. Containers: europepmc_supplementary_zip 3ecf626259edf3ee82a10b76a20be078382d4e7ecb4b4fa5145143c4d5ccbf51; cancers-13-06283-s001.zip 0fd70ccaf67605cfa4a05a6f65666bfa16812c75ac53f865860b6e8e7eb9deac. The Europe PMC zip is rebuilt per request, so its hash describes one retrieval only. |
| attributes.version Haraksingh et al. 2017 high-confidence NA12878 CNV list (2,076 CNVs, 51-453,313 bp) Context-only references | A Comparison of Tools for Copy-Number Variation Detection in Germline Whole Exome and Whole Genome Sequencing Data Methods 2.1 and 2.5; Table S2 rows 'GB-WGS-NA12878' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Cancers 13(24):6283, published 2021-12-14; PMC8699073 full-text XML | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.version Haraksingh et al. 2017 high-confidence NA12878 CNV list (2,076 CNVs, 51-453,313 bp) Context-only references | Gabrielaite et al. 2021, Table S2 (precision and recall of CNV calling tools) Methods 2.1 and 2.5; Table S2 rows 'GB-WGS-NA12878' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Supplementary Materials/Table S2.xlsx inside cancers-13-06283-s001.zip | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: artifact_sha256 is the inner supplementary file. Containers: europepmc_supplementary_zip 3ecf626259edf3ee82a10b76a20be078382d4e7ecb4b4fa5145143c4d5ccbf51; cancers-13-06283-s001.zip 0fd70ccaf67605cfa4a05a6f65666bfa16812c75ac53f865860b6e8e7eb9deac. The Europe PMC zip is rebuilt per request, so its hash describes one retrieval only. |
| description Gold-standard sample in the Gabrielaite et al. benchmark. Context-only references | A Comparison of Tools for Copy-Number Variation Detection in Germline Whole Exome and Whole Genome Sequencing Data Methods 2.1 and 2.5; Table S2 rows 'GB-WGS-NA12878' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Cancers 13(24):6283, published 2021-12-14; PMC8699073 full-text XML | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| description Gold-standard sample in the Gabrielaite et al. benchmark. Context-only references | Gabrielaite et al. 2021, Table S2 (precision and recall of CNV calling tools) Methods 2.1 and 2.5; Table S2 rows 'GB-WGS-NA12878' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Supplementary Materials/Table S2.xlsx inside cancers-13-06283-s001.zip | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: artifact_sha256 is the inner supplementary file. Containers: europepmc_supplementary_zip 3ecf626259edf3ee82a10b76a20be078382d4e7ecb4b4fa5145143c4d5ccbf51; cancers-13-06283-s001.zip 0fd70ccaf67605cfa4a05a6f65666bfa16812c75ac53f865860b6e8e7eb9deac. The Europe PMC zip is rebuilt per request, so its hash describes one retrieval only. |
Release 2026-10-09-9307685239b3 · Record review: source checked
Stable ID: cnv-20261009-data-gabrielaite2021-na12878-wgs