Configuration

Varscan2 2.3.9 (Guille et al. 2025)

Varscan2 as run in the cited comparison.

Overview

Varscan2 as run in the cited comparison.

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

Evaluations and results

2 evaluations · 12 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: Varscan2 2.3.9 (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	0.414 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 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'), H29; Tools 'Varscan2'; column 'F1'
Configuration: Varscan2 2.3.9 (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	61 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 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'), E29; Tools 'Varscan2'; column 'FP'
Configuration: Varscan2 2.3.9 (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	4.05e-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 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'), G29; Tools 'Varscan2'; column 'FPR'
Configuration: Varscan2 2.3.9 (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	0.322 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 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'), I29; Tools 'Varscan2'; column 'PPV'
Configuration: Varscan2 2.3.9 (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	0.58 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 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'), F29; Tools 'Varscan2'; column 'TPR'
Configuration: Varscan2 2.3.9 (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	29 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 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'), D29; Tools 'Varscan2'; column 'TP'
Configuration: Varscan2 2.3.9 (Guille et al. 2025)	Protocol: SEQC2 HCC1395 WES validation sample, somatic SNVs (Guille et al. 2025 Table S7) Dataset: SEQC2 HCC1395/HCC1395BL WES, Fudan replicate (WES_FD_T_1), high-confidence regions	0.733 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 Varscan2 on SEQC2 HCC1395 WES validation SNVs (Guille et al. 2025) somatic-20261009-protocol-guille2025-seqc2-fd-wes-snv 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'), H12; Tools 'Varscan2'; column 'F1'
Configuration: Varscan2 2.3.9 (Guille et al. 2025)	Protocol: SEQC2 HCC1395 WES validation sample, somatic SNVs (Guille et al. 2025 Table S7) Dataset: SEQC2 HCC1395/HCC1395BL WES, Fudan replicate (WES_FD_T_1), high-confidence regions	75 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 Varscan2 on SEQC2 HCC1395 WES validation SNVs (Guille et al. 2025) somatic-20261009-protocol-guille2025-seqc2-fd-wes-snv 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'), E12; Tools 'Varscan2'; column 'FP'
Configuration: Varscan2 2.3.9 (Guille et al. 2025)	Protocol: SEQC2 HCC1395 WES validation sample, somatic SNVs (Guille et al. 2025 Table S7) Dataset: SEQC2 HCC1395/HCC1395BL WES, Fudan replicate (WES_FD_T_1), high-confidence regions	4.98e-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 Varscan2 on SEQC2 HCC1395 WES validation SNVs (Guille et al. 2025) somatic-20261009-protocol-guille2025-seqc2-fd-wes-snv 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'), G12; Tools 'Varscan2'; column 'FPR'
Configuration: Varscan2 2.3.9 (Guille et al. 2025)	Protocol: SEQC2 HCC1395 WES validation sample, somatic SNVs (Guille et al. 2025 Table S7) Dataset: SEQC2 HCC1395/HCC1395BL WES, Fudan replicate (WES_FD_T_1), high-confidence regions	0.905 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 Varscan2 on SEQC2 HCC1395 WES validation SNVs (Guille et al. 2025) somatic-20261009-protocol-guille2025-seqc2-fd-wes-snv 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'), I12; Tools 'Varscan2'; column 'PPV'
Configuration: Varscan2 2.3.9 (Guille et al. 2025)	Protocol: SEQC2 HCC1395 WES validation sample, somatic SNVs (Guille et al. 2025 Table S7) Dataset: SEQC2 HCC1395/HCC1395BL WES, Fudan replicate (WES_FD_T_1), high-confidence regions	0.616 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 Varscan2 on SEQC2 HCC1395 WES validation SNVs (Guille et al. 2025) somatic-20261009-protocol-guille2025-seqc2-fd-wes-snv 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'), F12; Tools 'Varscan2'; column 'TPR'
Configuration: Varscan2 2.3.9 (Guille et al. 2025)	Protocol: SEQC2 HCC1395 WES validation sample, somatic SNVs (Guille et al. 2025 Table S7) Dataset: SEQC2 HCC1395/HCC1395BL WES, Fudan replicate (WES_FD_T_1), high-confidence regions	715 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 Varscan2 on SEQC2 HCC1395 WES validation SNVs (Guille et al. 2025) somatic-20261009-protocol-guille2025-seqc2-fd-wes-snv 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'), D12; Tools 'Varscan2'; column 'TP'

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Release 2026-10-09-8cc1db47c7f9 · Record review: source checked

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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 methods (caller command lines) · Original source · supplementary_methods_bbae697.docx inside the Europe PMC supplementary files bundle for PMC11790059
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-varscan2

areas: dna-genomes
contexts: clinical_research
method types: conventional_pipeline
reported name: Varscan2
version: 2.3.9
protocol: Paired tumour-normal WES calling restricted to target regions; command line and parameters in the supplementary methods (section '#Varscan2')
foundation model eligible: false
source locator: Table 1 row 'Varscan2'; Supplementary Table S7 row label 'Varscan2'; supplementary methods

Related records

configuration of: VarScan
system: Varscan2 on SEQC2 HCC1395 WES validation indels (Guille et al. 2025)
system: Varscan2 on SEQC2 HCC1395 WES validation SNVs (Guille et al. 2025)

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