Protocol

SEQC2 HCC1395 WES validation sample, somatic indels (Guille et al. 2025 Table S7)

Per-caller and retained-ensemble TP, FP, recall, false-positive rate, precision and F1 for somatic indels.

Overview

Per-caller and retained-ensemble TP, FP, recall, false-positive rate, precision and F1 for somatic indels.

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

15 recorded evaluations, 90 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

15 evaluations · 90 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: DeepSomatic-WES 1.7.0 (Guille et al. 2025)	Protocol: SEQC2 HCC1395 WES validation sample, somatic indels (Guille et al. 2025 Table S7) Dataset: SEQC2 HCC1395/HCC1395BL WES, Fudan replicate (WES_FD_T_1), high-confidence regions	0.812 f1-score fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DeepSomatic-WES on SEQC2 HCC1395 WES validation indels (Guille et al. 2025) somatic-20261009-protocol-guille2025-seqc2-fd-wes-indel Aggregation: Not reported A benchmarking study of individual somatic variant callers and voting-based ensembles for whole-exome sequencing; Guille et al. 2025, Supplementary Table S7 (validation dataset) · Supplementary Table S7 (tables7_bbae697.xls, sheet 'Results'), H32; Tools 'DeepSomatic-WES'; column 'F1'
Configuration: DeepSomatic-WES 1.7.0 (Guille et al. 2025)	Protocol: SEQC2 HCC1395 WES validation sample, somatic indels (Guille et al. 2025 Table S7) Dataset: SEQC2 HCC1395/HCC1395BL WES, Fudan replicate (WES_FD_T_1), high-confidence regions	10 false-positive-count count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DeepSomatic-WES on SEQC2 HCC1395 WES validation indels (Guille et al. 2025) somatic-20261009-protocol-guille2025-seqc2-fd-wes-indel Aggregation: Not reported A benchmarking study of individual somatic variant callers and voting-based ensembles for whole-exome sequencing; Guille et al. 2025, Supplementary Table S7 (validation dataset) · Supplementary Table S7 (tables7_bbae697.xls, sheet 'Results'), E32; Tools 'DeepSomatic-WES'; column 'FP'
Configuration: DeepSomatic-WES 1.7.0 (Guille et al. 2025)	Protocol: SEQC2 HCC1395 WES validation sample, somatic indels (Guille et al. 2025 Table S7) Dataset: SEQC2 HCC1395/HCC1395BL WES, Fudan replicate (WES_FD_T_1), high-confidence regions	6.64e-8 false-positive-rate fraction · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DeepSomatic-WES on SEQC2 HCC1395 WES validation indels (Guille et al. 2025) somatic-20261009-protocol-guille2025-seqc2-fd-wes-indel Aggregation: Not reported A benchmarking study of individual somatic variant callers and voting-based ensembles for whole-exome sequencing; Guille et al. 2025, Supplementary Table S7 (validation dataset) · Supplementary Table S7 (tables7_bbae697.xls, sheet 'Results'), G32; Tools 'DeepSomatic-WES'; column 'FPR'
Configuration: DeepSomatic-WES 1.7.0 (Guille et al. 2025)	Protocol: SEQC2 HCC1395 WES validation sample, somatic indels (Guille et al. 2025 Table S7) Dataset: SEQC2 HCC1395/HCC1395BL WES, Fudan replicate (WES_FD_T_1), high-confidence regions	0.804 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 DeepSomatic-WES on SEQC2 HCC1395 WES validation indels (Guille et al. 2025) somatic-20261009-protocol-guille2025-seqc2-fd-wes-indel Aggregation: Not reported A benchmarking study of individual somatic variant callers and voting-based ensembles for whole-exome sequencing; Guille et al. 2025, Supplementary Table S7 (validation dataset) · Supplementary Table S7 (tables7_bbae697.xls, sheet 'Results'), I32; Tools 'DeepSomatic-WES'; column 'PPV'
Configuration: DeepSomatic-WES 1.7.0 (Guille et al. 2025)	Protocol: SEQC2 HCC1395 WES validation sample, somatic indels (Guille et al. 2025 Table S7) Dataset: SEQC2 HCC1395/HCC1395BL WES, Fudan replicate (WES_FD_T_1), high-confidence regions	0.82 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 DeepSomatic-WES on SEQC2 HCC1395 WES validation indels (Guille et al. 2025) somatic-20261009-protocol-guille2025-seqc2-fd-wes-indel Aggregation: Not reported A benchmarking study of individual somatic variant callers and voting-based ensembles for whole-exome sequencing; Guille et al. 2025, Supplementary Table S7 (validation dataset) · Supplementary Table S7 (tables7_bbae697.xls, sheet 'Results'), F32; Tools 'DeepSomatic-WES'; column 'TPR'
Configuration: DeepSomatic-WES 1.7.0 (Guille et al. 2025)	Protocol: SEQC2 HCC1395 WES validation sample, somatic indels (Guille et al. 2025 Table S7) Dataset: SEQC2 HCC1395/HCC1395BL WES, Fudan replicate (WES_FD_T_1), high-confidence regions	41 true-positive-count count · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DeepSomatic-WES on SEQC2 HCC1395 WES validation indels (Guille et al. 2025) somatic-20261009-protocol-guille2025-seqc2-fd-wes-indel Aggregation: Not reported A benchmarking study of individual somatic variant callers and voting-based ensembles for whole-exome sequencing; Guille et al. 2025, Supplementary Table S7 (validation dataset) · Supplementary Table S7 (tables7_bbae697.xls, sheet 'Results'), D32; Tools 'DeepSomatic-WES'; column 'TP'
Configuration: FreeBayes 1.3.4 (Guille et al. 2025)	Protocol: SEQC2 HCC1395 WES validation sample, somatic indels (Guille et al. 2025 Table S7) Dataset: SEQC2 HCC1395/HCC1395BL WES, Fudan replicate (WES_FD_T_1), high-confidence regions	0.178 f1-score fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source FreeBayes on SEQC2 HCC1395 WES validation indels (Guille et al. 2025) somatic-20261009-protocol-guille2025-seqc2-fd-wes-indel Aggregation: Not reported A benchmarking study of individual somatic variant callers and voting-based ensembles for whole-exome sequencing; Guille et al. 2025, Supplementary Table S7 (validation dataset) · Supplementary Table S7 (tables7_bbae697.xls, sheet 'Results'), H22; Tools 'FreeBayes'; column 'F1'
Configuration: FreeBayes 1.3.4 (Guille et al. 2025)	Protocol: SEQC2 HCC1395 WES validation sample, somatic indels (Guille et al. 2025 Table S7) Dataset: SEQC2 HCC1395/HCC1395BL WES, Fudan replicate (WES_FD_T_1), high-confidence regions	226 false-positive-count count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source FreeBayes on SEQC2 HCC1395 WES validation indels (Guille et al. 2025) somatic-20261009-protocol-guille2025-seqc2-fd-wes-indel Aggregation: Not reported A benchmarking study of individual somatic variant callers and voting-based ensembles for whole-exome sequencing; Guille et al. 2025, Supplementary Table S7 (validation dataset) · Supplementary Table S7 (tables7_bbae697.xls, sheet 'Results'), E22; Tools 'FreeBayes'; column 'FP'
Configuration: FreeBayes 1.3.4 (Guille et al. 2025)	Protocol: SEQC2 HCC1395 WES validation sample, somatic indels (Guille et al. 2025 Table S7) Dataset: SEQC2 HCC1395/HCC1395BL WES, Fudan replicate (WES_FD_T_1), high-confidence regions	0.0000015 false-positive-rate fraction · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source FreeBayes on SEQC2 HCC1395 WES validation indels (Guille et al. 2025) somatic-20261009-protocol-guille2025-seqc2-fd-wes-indel Aggregation: Not reported A benchmarking study of individual somatic variant callers and voting-based ensembles for whole-exome sequencing; Guille et al. 2025, Supplementary Table S7 (validation dataset) · Supplementary Table S7 (tables7_bbae697.xls, sheet 'Results'), G22; Tools 'FreeBayes'; column 'FPR'
Configuration: FreeBayes 1.3.4 (Guille et al. 2025)	Protocol: SEQC2 HCC1395 WES validation sample, somatic indels (Guille et al. 2025 Table S7) Dataset: SEQC2 HCC1395/HCC1395BL WES, Fudan replicate (WES_FD_T_1), high-confidence regions	0.107 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 FreeBayes on SEQC2 HCC1395 WES validation indels (Guille et al. 2025) somatic-20261009-protocol-guille2025-seqc2-fd-wes-indel Aggregation: Not reported A benchmarking study of individual somatic variant callers and voting-based ensembles for whole-exome sequencing; Guille et al. 2025, Supplementary Table S7 (validation dataset) · Supplementary Table S7 (tables7_bbae697.xls, sheet 'Results'), I22; Tools 'FreeBayes'; column 'PPV'
Configuration: FreeBayes 1.3.4 (Guille et al. 2025)	Protocol: SEQC2 HCC1395 WES validation sample, somatic indels (Guille et al. 2025 Table S7) Dataset: SEQC2 HCC1395/HCC1395BL WES, Fudan replicate (WES_FD_T_1), high-confidence regions	0.54 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 FreeBayes on SEQC2 HCC1395 WES validation indels (Guille et al. 2025) somatic-20261009-protocol-guille2025-seqc2-fd-wes-indel Aggregation: Not reported A benchmarking study of individual somatic variant callers and voting-based ensembles for whole-exome sequencing; Guille et al. 2025, Supplementary Table S7 (validation dataset) · Supplementary Table S7 (tables7_bbae697.xls, sheet 'Results'), F22; Tools 'FreeBayes'; column 'TPR'
Configuration: FreeBayes 1.3.4 (Guille et al. 2025)	Protocol: SEQC2 HCC1395 WES validation sample, somatic indels (Guille et al. 2025 Table S7) Dataset: SEQC2 HCC1395/HCC1395BL WES, Fudan replicate (WES_FD_T_1), high-confidence regions	27 true-positive-count count · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source FreeBayes on SEQC2 HCC1395 WES validation indels (Guille et al. 2025) somatic-20261009-protocol-guille2025-seqc2-fd-wes-indel Aggregation: Not reported A benchmarking study of individual somatic variant callers and voting-based ensembles for whole-exome sequencing; Guille et al. 2025, Supplementary Table S7 (validation dataset) · Supplementary Table S7 (tables7_bbae697.xls, sheet 'Results'), D22; Tools 'FreeBayes'; column 'TP'
Configuration: Lancet 1.1.0 (Guille et al. 2025)	Protocol: SEQC2 HCC1395 WES validation sample, somatic indels (Guille et al. 2025 Table S7) Dataset: SEQC2 HCC1395/HCC1395BL WES, Fudan replicate (WES_FD_T_1), high-confidence regions	0.463 f1-score fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Lancet on SEQC2 HCC1395 WES validation indels (Guille et al. 2025) somatic-20261009-protocol-guille2025-seqc2-fd-wes-indel Aggregation: Not reported A benchmarking study of individual somatic variant callers and voting-based ensembles for whole-exome sequencing; Guille et al. 2025, Supplementary Table S7 (validation dataset) · Supplementary Table S7 (tables7_bbae697.xls, sheet 'Results'), H31; Tools 'Lancet'; column 'F1'
Configuration: Lancet 1.1.0 (Guille et al. 2025)	Protocol: SEQC2 HCC1395 WES validation sample, somatic indels (Guille et al. 2025 Table S7) Dataset: SEQC2 HCC1395/HCC1395BL WES, Fudan replicate (WES_FD_T_1), high-confidence regions	73 false-positive-count count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Lancet on SEQC2 HCC1395 WES validation indels (Guille et al. 2025) somatic-20261009-protocol-guille2025-seqc2-fd-wes-indel Aggregation: Not reported A benchmarking study of individual somatic variant callers and voting-based ensembles for whole-exome sequencing; Guille et al. 2025, Supplementary Table S7 (validation dataset) · Supplementary Table S7 (tables7_bbae697.xls, sheet 'Results'), E31; Tools 'Lancet'; column 'FP'
Configuration: Lancet 1.1.0 (Guille et al. 2025)	Protocol: SEQC2 HCC1395 WES validation sample, somatic indels (Guille et al. 2025 Table S7) Dataset: SEQC2 HCC1395/HCC1395BL WES, Fudan replicate (WES_FD_T_1), high-confidence regions	4.85e-7 false-positive-rate fraction · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Lancet on SEQC2 HCC1395 WES validation indels (Guille et al. 2025) somatic-20261009-protocol-guille2025-seqc2-fd-wes-indel Aggregation: Not reported A benchmarking study of individual somatic variant callers and voting-based ensembles for whole-exome sequencing; Guille et al. 2025, Supplementary Table S7 (validation dataset) · Supplementary Table S7 (tables7_bbae697.xls, sheet 'Results'), G31; Tools 'Lancet'; column 'FPR'
Configuration: Lancet 1.1.0 (Guille et al. 2025)	Protocol: SEQC2 HCC1395 WES validation sample, somatic indels (Guille et al. 2025 Table S7) Dataset: SEQC2 HCC1395/HCC1395BL WES, Fudan replicate (WES_FD_T_1), high-confidence regions	0.336 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 Lancet on SEQC2 HCC1395 WES validation indels (Guille et al. 2025) somatic-20261009-protocol-guille2025-seqc2-fd-wes-indel Aggregation: Not reported A benchmarking study of individual somatic variant callers and voting-based ensembles for whole-exome sequencing; Guille et al. 2025, Supplementary Table S7 (validation dataset) · Supplementary Table S7 (tables7_bbae697.xls, sheet 'Results'), I31; Tools 'Lancet'; column 'PPV'
Configuration: Lancet 1.1.0 (Guille et al. 2025)	Protocol: SEQC2 HCC1395 WES validation sample, somatic indels (Guille et al. 2025 Table S7) Dataset: SEQC2 HCC1395/HCC1395BL WES, Fudan replicate (WES_FD_T_1), high-confidence regions	0.74 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 Lancet on SEQC2 HCC1395 WES validation indels (Guille et al. 2025) somatic-20261009-protocol-guille2025-seqc2-fd-wes-indel Aggregation: Not reported A benchmarking study of individual somatic variant callers and voting-based ensembles for whole-exome sequencing; Guille et al. 2025, Supplementary Table S7 (validation dataset) · Supplementary Table S7 (tables7_bbae697.xls, sheet 'Results'), F31; Tools 'Lancet'; column 'TPR'
Configuration: Lancet 1.1.0 (Guille et al. 2025)	Protocol: SEQC2 HCC1395 WES validation sample, somatic indels (Guille et al. 2025 Table S7) Dataset: SEQC2 HCC1395/HCC1395BL WES, Fudan replicate (WES_FD_T_1), high-confidence regions	37 true-positive-count count · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Lancet on SEQC2 HCC1395 WES validation indels (Guille et al. 2025) somatic-20261009-protocol-guille2025-seqc2-fd-wes-indel Aggregation: Not reported A benchmarking study of individual somatic variant callers and voting-based ensembles for whole-exome sequencing; Guille et al. 2025, Supplementary Table S7 (validation dataset) · Supplementary Table S7 (tables7_bbae697.xls, sheet 'Results'), D31; Tools 'Lancet'; column 'TP'
Configuration: Lofreq 2.1.5 (Guille et al. 2025)	Protocol: SEQC2 HCC1395 WES validation sample, somatic indels (Guille et al. 2025 Table S7) Dataset: SEQC2 HCC1395/HCC1395BL WES, Fudan replicate (WES_FD_T_1), high-confidence regions	0.327 f1-score fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Lofreq on SEQC2 HCC1395 WES validation indels (Guille et al. 2025) somatic-20261009-protocol-guille2025-seqc2-fd-wes-indel Aggregation: Not reported A benchmarking study of individual somatic variant callers and voting-based ensembles for whole-exome sequencing; Guille et al. 2025, Supplementary Table S7 (validation dataset) · Supplementary Table S7 (tables7_bbae697.xls, sheet 'Results'), H23; Tools 'Lofreq'; column 'F1'
Configuration: Lofreq 2.1.5 (Guille et al. 2025)	Protocol: SEQC2 HCC1395 WES validation sample, somatic indels (Guille et al. 2025 Table S7) Dataset: SEQC2 HCC1395/HCC1395BL WES, Fudan replicate (WES_FD_T_1), high-confidence regions	155 false-positive-count count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Lofreq on SEQC2 HCC1395 WES validation indels (Guille et al. 2025) somatic-20261009-protocol-guille2025-seqc2-fd-wes-indel Aggregation: Not reported A benchmarking study of individual somatic variant callers and voting-based ensembles for whole-exome sequencing; Guille et al. 2025, Supplementary Table S7 (validation dataset) · Supplementary Table S7 (tables7_bbae697.xls, sheet 'Results'), E23; Tools 'Lofreq'; column 'FP'
Configuration: Lofreq 2.1.5 (Guille et al. 2025)	Protocol: SEQC2 HCC1395 WES validation sample, somatic indels (Guille et al. 2025 Table S7) Dataset: SEQC2 HCC1395/HCC1395BL WES, Fudan replicate (WES_FD_T_1), high-confidence regions	0.00000103 false-positive-rate fraction · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Lofreq on SEQC2 HCC1395 WES validation indels (Guille et al. 2025) somatic-20261009-protocol-guille2025-seqc2-fd-wes-indel Aggregation: Not reported A benchmarking study of individual somatic variant callers and voting-based ensembles for whole-exome sequencing; Guille et al. 2025, Supplementary Table S7 (validation dataset) · Supplementary Table S7 (tables7_bbae697.xls, sheet 'Results'), G23; Tools 'Lofreq'; column 'FPR'
Configuration: Lofreq 2.1.5 (Guille et al. 2025)	Protocol: SEQC2 HCC1395 WES validation sample, somatic indels (Guille et al. 2025 Table S7) Dataset: SEQC2 HCC1395/HCC1395BL WES, Fudan replicate (WES_FD_T_1), high-confidence regions	0.205 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 Lofreq on SEQC2 HCC1395 WES validation indels (Guille et al. 2025) somatic-20261009-protocol-guille2025-seqc2-fd-wes-indel Aggregation: Not reported A benchmarking study of individual somatic variant callers and voting-based ensembles for whole-exome sequencing; Guille et al. 2025, Supplementary Table S7 (validation dataset) · Supplementary Table S7 (tables7_bbae697.xls, sheet 'Results'), I23; Tools 'Lofreq'; column 'PPV'
Configuration: Lofreq 2.1.5 (Guille et al. 2025)	Protocol: SEQC2 HCC1395 WES validation sample, somatic indels (Guille et al. 2025 Table S7) Dataset: SEQC2 HCC1395/HCC1395BL WES, Fudan replicate (WES_FD_T_1), high-confidence regions	0.8 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 Lofreq on SEQC2 HCC1395 WES validation indels (Guille et al. 2025) somatic-20261009-protocol-guille2025-seqc2-fd-wes-indel Aggregation: Not reported A benchmarking study of individual somatic variant callers and voting-based ensembles for whole-exome sequencing; Guille et al. 2025, Supplementary Table S7 (validation dataset) · Supplementary Table S7 (tables7_bbae697.xls, sheet 'Results'), F23; Tools 'Lofreq'; column 'TPR'
Configuration: Lofreq 2.1.5 (Guille et al. 2025)	Protocol: SEQC2 HCC1395 WES validation sample, somatic indels (Guille et al. 2025 Table S7) Dataset: SEQC2 HCC1395/HCC1395BL WES, Fudan replicate (WES_FD_T_1), high-confidence regions	40 true-positive-count count · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Lofreq on SEQC2 HCC1395 WES validation indels (Guille et al. 2025) somatic-20261009-protocol-guille2025-seqc2-fd-wes-indel Aggregation: Not reported A benchmarking study of individual somatic variant callers and voting-based ensembles for whole-exome sequencing; Guille et al. 2025, Supplementary Table S7 (validation dataset) · Supplementary Table S7 (tables7_bbae697.xls, sheet 'Results'), D23; Tools 'Lofreq'; column 'TP'
Configuration: Mutect2 4.2.2.0 (Guille et al. 2025)	Protocol: SEQC2 HCC1395 WES validation sample, somatic indels (Guille et al. 2025 Table S7) Dataset: SEQC2 HCC1395/HCC1395BL WES, Fudan replicate (WES_FD_T_1), high-confidence regions	0.65 f1-score fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Mutect2 on SEQC2 HCC1395 WES validation indels (Guille et al. 2025) somatic-20261009-protocol-guille2025-seqc2-fd-wes-indel Aggregation: Not reported A benchmarking study of individual somatic variant callers and voting-based ensembles for whole-exome sequencing; Guille et al. 2025, Supplementary Table S7 (validation dataset) · Supplementary Table S7 (tables7_bbae697.xls, sheet 'Results'), H24; Tools 'Mutect2'; column 'F1'

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A benchmarking study of individual somatic variant callers and voting-based ensembles for whole-exome sequencing · Original source · Briefings in Bioinformatics 26(1):bbae697, published online 2025-01-18; PMC11790059 full-text XML
Guille et al. 2025, Supplementary Table S7 (validation dataset) · Original source · tables7_bbae697.xls inside the Europe PMC supplementary files bundle for PMC11790059

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Technical metadata and extraction receipts

Stable ID: somatic-20261009-protocol-guille2025-seqc2-fd-wes-indel

areas: dna-genomes
contexts: clinical_research
protocol: bwa mem alignment, callers run in paired tumour-normal mode on target regions, calls compared with the SEQC2 truth set in high-confidence regions. TPR = TP/(TP+FN), PPV = TP/(TP+FP), F1 = 2TP/(2TP+FP+FN).
version: Supplementary Table S7, Type of variant 'INDEL'
denominator: 50
limitations: Single WES sample of one cell line; no replicate or interval estimates.; Small truth set: 50 indels in SEQC2 high-confidence regions, so one variant moves recall by 0.02.; Not fully independent of development: the ensembles were selected on four datasets that include another WES replicate of the same HCC1395 pair with the same truth set (Table 2 row 'SEQC2').; Post-alignment procedure for Table S7 is not stated (Tables S1-S2 compare four procedures on the development datasets).; DeepSomatic and NeuSomatic pre-trained models were built with SEQC2 HCC1395 data (Discussion paragraph 5; supplementary methods checkpoint name), so their rows are not held out.; The authors' 'best individual tool' comparison in Results 'Validation' covers the classic callers only (gains of 2.7 and 10.2 points over Mutect and Mutect2); it excludes the deep-learning callers, as the ensemble search did (Methods 'Ensemble approach').
missing metadata: metric implementation: reason: unreported; note: Comparison tool for matching calls to the truth set is not named; FPR denominator is not defined
source locator: Supplementary Table S7; Methods 'Evaluation and metrics' and 'SEQC2 dataset'

Related records

uses data: SEQC2 HCC1395/HCC1395BL WES, Fudan replicate (WES_FD_T_1), high-confidence regions
assessment: DeepSomatic-WES on SEQC2 HCC1395 WES validation indels (Guille et al. 2025)
assessment: FreeBayes on SEQC2 HCC1395 WES validation indels (Guille et al. 2025)
assessment: Lancet on SEQC2 HCC1395 WES validation indels (Guille et al. 2025)
assessment: Lofreq on SEQC2 HCC1395 WES validation indels (Guille et al. 2025)
assessment: Mutect2 on SEQC2 HCC1395 WES validation indels (Guille et al. 2025)
assessment: NeuSomatic on SEQC2 HCC1395 WES validation indels (Guille et al. 2025)
assessment: Pindel on SEQC2 HCC1395 WES validation indels (Guille et al. 2025)
assessment: Scalpel on SEQC2 HCC1395 WES validation indels (Guille et al. 2025)
assessment: Seurat on SEQC2 HCC1395 WES validation indels (Guille et al. 2025)
assessment: Strelka on SEQC2 HCC1395 WES validation indels (Guille et al. 2025)
assessment: Vardict on SEQC2 HCC1395 WES validation indels (Guille et al. 2025)
assessment: VarNet on SEQC2 HCC1395 WES validation indels (Guille et al. 2025)
assessment: Varscan2 on SEQC2 HCC1395 WES validation indels (Guille et al. 2025)
assessment: Mutect2-Strelka-Varscan2 on SEQC2 HCC1395 WES validation indels (Guille et al. 2025)
assessment: Mutect2-Strelka-Pindel-Varscan2 on SEQC2 HCC1395 WES validation indels (Guille et al. 2025)
assessed by: Select a tumour DNA somatic variant-calling workflow

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