Configuration

Vote ensemble Mutect2, Strelka, Pindel, Varscan2, at least 2 agree (Guille et al. 2025)

Voting ensemble 'Mutect2-Strelka-Pindel-Varscan2' retained by the authors (Best-Comb-INDEL).

Overview

Voting ensemble 'Mutect2-Strelka-Pindel-Varscan2' retained by the authors (Best-Comb-INDEL).

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Evaluations and results

1 evaluation · 6 results. Different protocols are not a single leaderboard.

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: Vote ensemble Mutect2, Strelka, Pindel, Varscan2, at least 2 agree (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	0.752 f1-score fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Mutect2-Strelka-Pindel-Varscan2 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'), H35; Tools 'Mutect2-Strelka-Pindel-Varscan2'; column 'F1'
Configuration: Vote ensemble Mutect2, Strelka, Pindel, Varscan2, at least 2 agree (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	13 false-positive-count count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Mutect2-Strelka-Pindel-Varscan2 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'), E35; Tools 'Mutect2-Strelka-Pindel-Varscan2'; column 'FP'
Configuration: Vote ensemble Mutect2, Strelka, Pindel, Varscan2, at least 2 agree (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	8.63e-8 false-positive-rate fraction · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Mutect2-Strelka-Pindel-Varscan2 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'), G35; Tools 'Mutect2-Strelka-Pindel-Varscan2'; column 'FPR'
Configuration: Vote ensemble Mutect2, Strelka, Pindel, Varscan2, at least 2 agree (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	0.745 precision fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Mutect2-Strelka-Pindel-Varscan2 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'), I35; Tools 'Mutect2-Strelka-Pindel-Varscan2'; column 'PPV'
Configuration: Vote ensemble Mutect2, Strelka, Pindel, Varscan2, at least 2 agree (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	0.76 recall fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Mutect2-Strelka-Pindel-Varscan2 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'), F35; Tools 'Mutect2-Strelka-Pindel-Varscan2'; column 'TPR'
Configuration: Vote ensemble Mutect2, Strelka, Pindel, Varscan2, at least 2 agree (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	38 true-positive-count count · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Mutect2-Strelka-Pindel-Varscan2 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'), D35; Tools 'Mutect2-Strelka-Pindel-Varscan2'; column 'TP'

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Sources and history

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2 source records and release history

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-config-guille2025-vote-4indel-min2

areas: dna-genomes
contexts: clinical_research
method types: conventional_pipeline
reported name: Mutect2-Strelka-Pindel-Varscan2
foundation model eligible: false
protocol: A variant is called when at least 2 of the 4 member callers report it; member caller versions as in Table 1
method role: Authors' own retained ensemble, selected on the four development datasets and then applied to the validation sample
selection: Table S7 category 'Best-Comb-INDEL'
source locator: Supplementary Table S7 row 'Mutect2-Strelka-Pindel-Varscan2'; Results 'Evaluation of the ensemble approach' and 'Validation'
missing metadata: version: reason: inapplicable; note: Ensemble of the listed caller versions

Related records

configuration of: Majority-vote consensus of somatic callers
system: Mutect2-Strelka-Pindel-Varscan2 on SEQC2 HCC1395 WES validation indels (Guille et al. 2025)

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