Configuration

Strelka2 2.9.10 via nf-core/sarek 3.5.0 (López-Cade et al. 2025)

Strelka2 2.9.10 via nf-core/sarek 3.5.0: nf-core/sarek 3.5.0 default parameters, tumour-normal mode, PASS SNVs.

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Evaluations and results

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

Protocol: Synthetic WES tumour-normal pair, 4,709 inserted COSMIC SNVs (López-Cade et al. 2025 Table 1) · Dataset: BAMSurgeon synthetic tumour-normal WES with 4,709 COSMIC SNVs (López-Cade et al. 2025)

Sorted by False negatives (SNV only, synthetic WES) (lower is better). The best value in each column is highlighted. Decimals are rounded for display; each value links to the printed value and its source.

Tested configuration	False negatives (SNV only, synthetic WES)	False positives (SNV only, synthetic WES)	Precision (SNV only, synthetic WES)	Recall (SNV only, synthetic WES)	True positives (SNV only, synthetic WES)	Count (SNV only, synthetic WES, total PASS calls)
Strelka2 2.9.10 via nf-core/sarek 3.5.0 (López-Cade et al. 2025)Evaluation	2531	1	1	0.463	2178	2179

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: Strelka2 2.9.10 via nf-core/sarek 3.5.0 (López-Cade et al. 2025)	Protocol: Synthetic WES tumour-normal pair, 4,709 inserted COSMIC SNVs (López-Cade et al. 2025 Table 1) Dataset: BAMSurgeon synthetic tumour-normal WES with 4,709 COSMIC SNVs (López-Cade et al. 2025)	2530 False negatives (SNV only, synthetic WES) count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Strelka2 on the synthetic WES pair (López-Cade et al. 2025) somatic-wes-synthetic-20261011-protocol-bamsurgeon-wes-snv Aggregation: Not reported Comparative Evaluation of Mutect2, Strelka2, and FreeBayes for Somatic SNV Detection in Synthetic and Clinical Whole-Exome Sequencing Data · Table 1, row 'Strelka2', column 'FN'
Configuration: Strelka2 2.9.10 via nf-core/sarek 3.5.0 (López-Cade et al. 2025)	Protocol: Synthetic WES tumour-normal pair, 4,709 inserted COSMIC SNVs (López-Cade et al. 2025 Table 1) Dataset: BAMSurgeon synthetic tumour-normal WES with 4,709 COSMIC SNVs (López-Cade et al. 2025)	1 False positives (SNV only, synthetic WES) count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Strelka2 on the synthetic WES pair (López-Cade et al. 2025) somatic-wes-synthetic-20261011-protocol-bamsurgeon-wes-snv Aggregation: Not reported Comparative Evaluation of Mutect2, Strelka2, and FreeBayes for Somatic SNV Detection in Synthetic and Clinical Whole-Exome Sequencing Data · Table 1, row 'Strelka2', column 'FP'
Configuration: Strelka2 2.9.10 via nf-core/sarek 3.5.0 (López-Cade et al. 2025)	Protocol: Synthetic WES tumour-normal pair, 4,709 inserted COSMIC SNVs (López-Cade et al. 2025 Table 1) Dataset: BAMSurgeon synthetic tumour-normal WES with 4,709 COSMIC SNVs (López-Cade et al. 2025)	1 Precision (SNV only, synthetic WES) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Strelka2 on the synthetic WES pair (López-Cade et al. 2025) somatic-wes-synthetic-20261011-protocol-bamsurgeon-wes-snv Aggregation: Not reported Comparative Evaluation of Mutect2, Strelka2, and FreeBayes for Somatic SNV Detection in Synthetic and Clinical Whole-Exome Sequencing Data · Table 1, row 'Strelka2', column 'Precision'
Configuration: Strelka2 2.9.10 via nf-core/sarek 3.5.0 (López-Cade et al. 2025)	Protocol: Synthetic WES tumour-normal pair, 4,709 inserted COSMIC SNVs (López-Cade et al. 2025 Table 1) Dataset: BAMSurgeon synthetic tumour-normal WES with 4,709 COSMIC SNVs (López-Cade et al. 2025)	0.463 Recall (SNV only, synthetic WES) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Strelka2 on the synthetic WES pair (López-Cade et al. 2025) somatic-wes-synthetic-20261011-protocol-bamsurgeon-wes-snv Aggregation: Not reported Comparative Evaluation of Mutect2, Strelka2, and FreeBayes for Somatic SNV Detection in Synthetic and Clinical Whole-Exome Sequencing Data · Table 1, row 'Strelka2', column 'Recall'
Configuration: Strelka2 2.9.10 via nf-core/sarek 3.5.0 (López-Cade et al. 2025)	Protocol: Synthetic WES tumour-normal pair, 4,709 inserted COSMIC SNVs (López-Cade et al. 2025 Table 1) Dataset: BAMSurgeon synthetic tumour-normal WES with 4,709 COSMIC SNVs (López-Cade et al. 2025)	2180 Count (SNV only, synthetic WES, total PASS calls) count · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Strelka2 on the synthetic WES pair (López-Cade et al. 2025) somatic-wes-synthetic-20261011-protocol-bamsurgeon-wes-snv Aggregation: Not reported Comparative Evaluation of Mutect2, Strelka2, and FreeBayes for Somatic SNV Detection in Synthetic and Clinical Whole-Exome Sequencing Data · Table 1, row 'Strelka2', column 'Total Query'
Configuration: Strelka2 2.9.10 via nf-core/sarek 3.5.0 (López-Cade et al. 2025)	Protocol: Synthetic WES tumour-normal pair, 4,709 inserted COSMIC SNVs (López-Cade et al. 2025 Table 1) Dataset: BAMSurgeon synthetic tumour-normal WES with 4,709 COSMIC SNVs (López-Cade et al. 2025)	2180 True positives (SNV only, synthetic WES) count · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Strelka2 on the synthetic WES pair (López-Cade et al. 2025) somatic-wes-synthetic-20261011-protocol-bamsurgeon-wes-snv Aggregation: Not reported Comparative Evaluation of Mutect2, Strelka2, and FreeBayes for Somatic SNV Detection in Synthetic and Clinical Whole-Exome Sequencing Data · Table 1, row 'Strelka2', column 'TP'

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Comparative Evaluation of Mutect2, Strelka2, and FreeBayes for Somatic SNV Detection in Synthetic and Clinical Whole-Exome Sequencing Data · Original source · Biomolecules 15(11):1532, published 2025-10-30; PMC12650410 full-text XML

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Technical metadata and extraction receipts

Stable ID: somatic-wes-synthetic-20261011-config-strelka2

areas: dna-genomes
contexts: clinical_research
method types: conventional_pipeline
reported name: Strelka2
foundation model eligible: false
parameters: nf-core/sarek 3.5.0 default parameters, tumour-normal mode, PASS SNVs
access reuse: Public open-source software
source locator: Methods 2.4 'Variant Calling and Bioinformatic Workflow'
version: 2.9.10
provenance note: Strelka2 as run in the cited comparison.

Related records

configuration of: Strelka
system: Strelka2 on the synthetic WES pair (López-Cade et al. 2025)

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