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FreeBayes 1.3.4 (Guille et al. 2025)

FreeBayes as run in the cited comparison.

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FreeBayes 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: 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: FreeBayes 1.3.4 (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	0.596 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 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'), H4; Tools 'FreeBayes'; column 'F1'
Configuration: FreeBayes 1.3.4 (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	883 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 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'), E4; Tools 'FreeBayes'; column 'FP'
Configuration: FreeBayes 1.3.4 (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	0.00000586 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 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'), G4; Tools 'FreeBayes'; column 'FPR'
Configuration: FreeBayes 1.3.4 (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	0.496 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 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'), I4; Tools 'FreeBayes'; column 'PPV'
Configuration: FreeBayes 1.3.4 (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	0.748 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 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'), F4; Tools 'FreeBayes'; column 'TPR'
Configuration: FreeBayes 1.3.4 (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	868 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 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'), D4; Tools 'FreeBayes'; 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-freebayes

areas: dna-genomes
contexts: clinical_research
method types: conventional_pipeline
reported name: FreeBayes
version: 1.3.4
protocol: Paired tumour-normal WES calling restricted to target regions; command line and parameters in the supplementary methods (section '#FreeBayes')
foundation model eligible: false
source locator: Table 1 row 'FreeBayes'; Supplementary Table S7 row label 'FreeBayes'; supplementary methods

Related records

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

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