Configuration

Lancet

Lancet; bounded primary-source AMP candidate.

Overview

Lancet; bounded primary-source AMP candidate.

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

Evaluations and results

1 evaluation · 12 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: 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 checked Methods, coverage and source Lancet evaluation 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. 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 checked Methods, coverage and source Lancet evaluation 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. 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 checked Methods, coverage and source Lancet evaluation 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. 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 checked Methods, coverage and source Lancet evaluation 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. 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 checked Methods, coverage and source Lancet evaluation 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. 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 checked Methods, coverage and source Lancet evaluation 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. 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 checked Methods, coverage and source Lancet evaluation 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. 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 checked Methods, coverage and source Lancet evaluation 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. 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 checked Methods, coverage and source Lancet evaluation 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. 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 checked Methods, coverage and source Lancet evaluation 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. 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 checked Methods, coverage and source Lancet evaluation 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. 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 checked Methods, coverage and source Lancet evaluation 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. 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.

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Claims, original sources and review scope · Release 2026-10-07-1448159e6a81
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Release 2026-10-07-1448159e6a81 · Record review: source checked

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Genome-wide somatic variant calling using localized colored de Bruijn graphs · Original source · Europe PMC fullTextXML retrieved 2026-10-07T12:24:27.822425+00:00

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Technical metadata and extraction receipts

Stable ID: amp-oncology-rna-20261007-issue-10-config-lancet

method types: conventional_pipeline
foundation model eligible: false
missing metadata: version: Exact caller release not extracted from the primary article; retain paper-era method identity, not a concrete current checkpoint.
reported name: Lancet
version: Not reported

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configuration: Lancet evaluation

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