Lancet evaluation; bounded primary-source AMP candidate.
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1 evaluation · 12 results. Different protocols are not a single leaderboard.
Applied filters: All linked evaluations
| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: Lancet | Protocol: Lancet paper virtual-tumor SNV/indel benchmark Dataset: NA12892/NA12891 virtual tumor and matched normal | 0.81 indel F1-score fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceSeparate SNV and indel virtual-tumor pairs; real germline-supporting reads swapped at reference-homozygous/alternate-homozygous loci; binomial VAF means 0.05, 0.1, 0.2, 0.3; insertion max 13 bp, deletion max 35 bp. Aggregation: Not reported Genome-wide somatic variant calling using localized colored de Bruijn graphs · Table 1, Lancet row (JATS Tab1) |
| Configuration: Lancet | Protocol: Lancet paper virtual-tumor SNV/indel benchmark Dataset: NA12892/NA12891 virtual tumor and matched normal | 1360 indel false negatives variants · lower Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceSeparate SNV and indel virtual-tumor pairs; real germline-supporting reads swapped at reference-homozygous/alternate-homozygous loci; binomial VAF means 0.05, 0.1, 0.2, 0.3; insertion max 13 bp, deletion max 35 bp. Aggregation: Not reported Genome-wide somatic variant calling using localized colored de Bruijn graphs · Table 1, Lancet row (JATS Tab1) |
| Configuration: Lancet | Protocol: Lancet paper virtual-tumor SNV/indel benchmark Dataset: NA12892/NA12891 virtual tumor and matched normal | 305 indel false positives variants · lower Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceSeparate SNV and indel virtual-tumor pairs; real germline-supporting reads swapped at reference-homozygous/alternate-homozygous loci; binomial VAF means 0.05, 0.1, 0.2, 0.3; insertion max 13 bp, deletion max 35 bp. Aggregation: Not reported Genome-wide somatic variant calling using localized colored de Bruijn graphs · Table 1, Lancet row (JATS Tab1) |
| Configuration: Lancet | Protocol: Lancet paper virtual-tumor SNV/indel benchmark Dataset: NA12892/NA12891 virtual tumor and matched normal | 0.92 indel precision fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceSeparate SNV and indel virtual-tumor pairs; real germline-supporting reads swapped at reference-homozygous/alternate-homozygous loci; binomial VAF means 0.05, 0.1, 0.2, 0.3; insertion max 13 bp, deletion max 35 bp. Aggregation: Not reported Genome-wide somatic variant calling using localized colored de Bruijn graphs · Table 1, Lancet row (JATS Tab1) |
| Configuration: Lancet | Protocol: Lancet paper virtual-tumor SNV/indel benchmark Dataset: NA12892/NA12891 virtual tumor and matched normal | 0.72 indel recall fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceSeparate SNV and indel virtual-tumor pairs; real germline-supporting reads swapped at reference-homozygous/alternate-homozygous loci; binomial VAF means 0.05, 0.1, 0.2, 0.3; insertion max 13 bp, deletion max 35 bp. Aggregation: Not reported Genome-wide somatic variant calling using localized colored de Bruijn graphs · Table 1, Lancet row (JATS Tab1) |
| Configuration: Lancet | Protocol: Lancet paper virtual-tumor SNV/indel benchmark Dataset: NA12892/NA12891 virtual tumor and matched normal | 3590 indel true positives variants · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceSeparate SNV and indel virtual-tumor pairs; real germline-supporting reads swapped at reference-homozygous/alternate-homozygous loci; binomial VAF means 0.05, 0.1, 0.2, 0.3; insertion max 13 bp, deletion max 35 bp. Aggregation: Not reported Genome-wide somatic variant calling using localized colored de Bruijn graphs · Table 1, Lancet row (JATS Tab1) |
| Configuration: Lancet | Protocol: Lancet paper virtual-tumor SNV/indel benchmark Dataset: NA12892/NA12891 virtual tumor and matched normal | 0.85 SNV F1-score fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceSeparate SNV and indel virtual-tumor pairs; real germline-supporting reads swapped at reference-homozygous/alternate-homozygous loci; binomial VAF means 0.05, 0.1, 0.2, 0.3; insertion max 13 bp, deletion max 35 bp. Aggregation: Not reported Genome-wide somatic variant calling using localized colored de Bruijn graphs · Table 2, Lancet row (JATS Tab2) |
| Configuration: Lancet | Protocol: Lancet paper virtual-tumor SNV/indel benchmark Dataset: NA12892/NA12891 virtual tumor and matched normal | 7740 SNV false negatives variants · lower Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceSeparate SNV and indel virtual-tumor pairs; real germline-supporting reads swapped at reference-homozygous/alternate-homozygous loci; binomial VAF means 0.05, 0.1, 0.2, 0.3; insertion max 13 bp, deletion max 35 bp. Aggregation: Not reported Genome-wide somatic variant calling using localized colored de Bruijn graphs · Table 2, Lancet row (JATS Tab2) |
| Configuration: Lancet | Protocol: Lancet paper virtual-tumor SNV/indel benchmark Dataset: NA12892/NA12891 virtual tumor and matched normal | 565 SNV false positives variants · lower Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceSeparate SNV and indel virtual-tumor pairs; real germline-supporting reads swapped at reference-homozygous/alternate-homozygous loci; binomial VAF means 0.05, 0.1, 0.2, 0.3; insertion max 13 bp, deletion max 35 bp. Aggregation: Not reported Genome-wide somatic variant calling using localized colored de Bruijn graphs · Table 2, Lancet row (JATS Tab2) |
| Configuration: Lancet | Protocol: Lancet paper virtual-tumor SNV/indel benchmark Dataset: NA12892/NA12891 virtual tumor and matched normal | 0.98 SNV precision fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceSeparate SNV and indel virtual-tumor pairs; real germline-supporting reads swapped at reference-homozygous/alternate-homozygous loci; binomial VAF means 0.05, 0.1, 0.2, 0.3; insertion max 13 bp, deletion max 35 bp. Aggregation: Not reported Genome-wide somatic variant calling using localized colored de Bruijn graphs · Table 2, Lancet row (JATS Tab2) |
| Configuration: Lancet | Protocol: Lancet paper virtual-tumor SNV/indel benchmark Dataset: NA12892/NA12891 virtual tumor and matched normal | 0.75 SNV recall fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceSeparate SNV and indel virtual-tumor pairs; real germline-supporting reads swapped at reference-homozygous/alternate-homozygous loci; binomial VAF means 0.05, 0.1, 0.2, 0.3; insertion max 13 bp, deletion max 35 bp. Aggregation: Not reported Genome-wide somatic variant calling using localized colored de Bruijn graphs · Table 2, Lancet row (JATS Tab2) |
| Configuration: Lancet | Protocol: Lancet paper virtual-tumor SNV/indel benchmark Dataset: NA12892/NA12891 virtual tumor and matched normal | 23,848 SNV true positives variants · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceSeparate SNV and indel virtual-tumor pairs; real germline-supporting reads swapped at reference-homozygous/alternate-homozygous loci; binomial VAF means 0.05, 0.1, 0.2, 0.3; insertion max 13 bp, deletion max 35 bp. Aggregation: Not reported Genome-wide somatic variant calling using localized colored de Bruijn graphs · Table 2, Lancet row (JATS Tab2) |
Source checking is not independent reproduction. Release 2026-10-07-1448159e6a81.
Separate SNV and indel virtual-tumor pairs; real germline-supporting reads swapped at reference-homozygous/alternate-homozygous loci; binomial VAF means 0.05, 0.1, 0.2, 0.3; insertion max 13 bp, deletion max 35 bp.
Metadata review: source checked. Unreported conditions prevent automatic comparisons.
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.
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One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.
17 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| attributes.comparison.adaptation Not reported Context-only references | Genome-wide somatic variant calling using localized colored de Bruijn graphs No field-specific location recorded Version: Europe PMC fullTextXML retrieved 2026-10-07T12:24:27.822425+00:00 | missing or unspecified No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.comparison.aggregation pooled variants separately for SNVs and indels Context-only references | Genome-wide somatic variant calling using localized colored de Bruijn graphs No field-specific location recorded Version: Europe PMC fullTextXML retrieved 2026-10-07T12:24:27.822425+00:00 | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.comparison.budget Not reported Context-only references | Genome-wide somatic variant calling using localized colored de Bruijn graphs No field-specific location recorded Version: Europe PMC fullTextXML retrieved 2026-10-07T12:24:27.822425+00:00 | missing or unspecified No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.comparison.dataset_version Not reported Context-only references | Genome-wide somatic variant calling using localized colored de Bruijn graphs No field-specific location recorded Version: Europe PMC fullTextXML retrieved 2026-10-07T12:24:27.822425+00:00 | missing or unspecified No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.comparison.inputs virtual-tumour and matched-normal aligned BAM Context-only references | Genome-wide somatic variant calling using localized colored de Bruijn graphs No field-specific location recorded Version: Europe PMC fullTextXML retrieved 2026-10-07T12:24:27.822425+00:00 | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.comparison.metric_implementation Not reported Context-only references | Genome-wide somatic variant calling using localized colored de Bruijn graphs No field-specific location recorded Version: Europe PMC fullTextXML retrieved 2026-10-07T12:24:27.822425+00:00 | missing or unspecified No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.comparison.population 31,592 SNVs / 4,945 indels Context-only references | Genome-wide somatic variant calling using localized colored de Bruijn graphs No field-specific location recorded Version: Europe PMC fullTextXML retrieved 2026-10-07T12:24:27.822425+00:00 | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.comparison.protocol_id Not reported Context-only references | Genome-wide somatic variant calling using localized colored de Bruijn graphs No field-specific location recorded Version: Europe PMC fullTextXML retrieved 2026-10-07T12:24:27.822425+00:00 | missing or unspecified No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.comparison.split Not reported Context-only references | Genome-wide somatic variant calling using localized colored de Bruijn graphs No field-specific location recorded Version: Europe PMC fullTextXML retrieved 2026-10-07T12:24:27.822425+00:00 | missing or unspecified No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.origin author_reported Context-only references | Genome-wide somatic variant calling using localized colored de Bruijn graphs No field-specific location recorded Version: Europe PMC fullTextXML retrieved 2026-10-07T12:24:27.822425+00:00 | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
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Release 2026-10-07-1448159e6a81 · Record review: source checked
Stable ID: amp-oncology-rna-20261007-issue-10-eval-lancet