Configuration

Strelka2 2.9.10 (Hasan 2026)

Strelka2 2.9.10: quay.io/biocontainers/strelka:2.9.10--h9ee0642_1, digest sha256:e6133fa935d444aaf3aa04b57256a580d9b3498298fc17cb5f4a9818116105ec5; PASS calls.

4 evaluations · 24 results

Overview

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

Evaluations and results

4 evaluations · 24 results. Different protocols are not a single leaderboard.

Dataset: NIST/GIAB HG008 tumour-normal WGS (HG008-T pancreatic cancer cell line, matched normal), HG008-T draft somatic small-variant benchmark v0.3

Sorted by F1 (indel only, HG008 primary region) (higher 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	Protocol and dataset	F1 (indel only, HG008 primary region)	F1 (SNV only, HG008 primary region)	F1 (SNVs and indels, HG008 all-benchmark region)	F1 (SNVs and indels, HG008 primary region)	False negatives (indel only, HG008 primary region)	False negatives (SNV only, HG008 primary region)	False negatives (SNVs and indels, HG008 all-benchmark region)	False negatives (SNVs and indels, HG008 primary region)	False positives (indel only, HG008 primary region)	False positives (SNV only, HG008 primary region)	False positives (SNVs and indels, HG008 all-benchmark region)	False positives (SNVs and indels, HG008 primary region)	Precision (indel only, HG008 primary region)	Precision (SNV only, HG008 primary region)	Precision (SNVs and indels, HG008 all-benchmark region)	Precision (SNVs and indels, HG008 primary region)	Recall (indel only, HG008 primary region)	Recall (SNV only, HG008 primary region)	Recall (SNVs and indels, HG008 all-benchmark region)	Recall (SNVs and indels, HG008 primary region)	True positives (indel only, HG008 primary region)	True positives (SNV only, HG008 primary region)	True positives (SNVs and indels, HG008 all-benchmark region)	True positives (SNVs and indels, HG008 primary region)
Strelka2 2.9.10 (Hasan 2026)Evaluation	HG008 primary region (nogermlineinterference), indels, Mutect2, Strelka2, DeepSomatic and ensembles (Hasan 2026 Table 2, Class 'INDEL')	0.691	Not reported	Not reported	Not reported	2074	Not reported	Not reported	Not reported	487	Not reported	Not reported	Not reported	0.855	Not reported	Not reported	Not reported	0.58	Not reported	Not reported	Not reported	2862	Not reported	Not reported	Not reported
Strelka2 2.9.10 (Hasan 2026)Evaluation	HG008 all-benchmark region (sensitivity analysis), SNVs and indels combined, Mutect2, Strelka2, DeepSomatic and ensembles (Hasan 2026 Table 4)	Not reported	Not reported	0.698	Not reported	Not reported	Not reported	6058	Not reported	Not reported	Not reported	4475	Not reported	Not reported	Not reported	0.731	Not reported	Not reported	Not reported	0.667	Not reported	Not reported	Not reported	12149	Not reported
Strelka2 2.9.10 (Hasan 2026)Evaluation	HG008 primary region (nogermlineinterference), SNVs and indels combined, Mutect2, Strelka2, DeepSomatic and ensembles (Hasan 2026 Table 1)	Not reported	Not reported	Not reported	0.779	Not reported	Not reported	Not reported	2257	Not reported	Not reported	Not reported	4414	Not reported	Not reported	Not reported	0.727	Not reported	Not reported	Not reported	0.839	Not reported	Not reported	Not reported	11757
Strelka2 2.9.10 (Hasan 2026)Evaluation	HG008 primary region (nogermlineinterference), SNVs, Mutect2, Strelka2, DeepSomatic and ensembles (Hasan 2026 Table 2, Class 'SNV')	Not reported	0.812	Not reported	Not reported	Not reported	183	Not reported	Not reported	Not reported	3927	Not reported	Not reported	Not reported	0.694	Not reported	Not reported	Not reported	0.98	Not reported	Not reported	Not reported	8895	Not reported	Not reported

All 24 result rows with coverage, uncertainty and sources

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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: Strelka2 2.9.10 (Hasan 2026)	Protocol: HG008 all-benchmark region (sensitivity analysis), SNVs and indels combined, Mutect2, Strelka2, DeepSomatic and ensembles (Hasan 2026 Table 4) Dataset: NIST/GIAB HG008 tumour-normal WGS (HG008-T pancreatic cancer cell line, matched normal), HG008-T draft somatic small-variant benchmark v0.3	0.698 F1 (SNVs and indels, HG008 all-benchmark region) fraction · higher Uncertainty: 95% CI 0.6691 to 0.7205. Genomic block bootstrap over 5-Mb blocks, linear percentile interval; prespecified, but executed after the primary external evaluation; spatial variation within the benchmark region, not between tumours Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Strelka2 on HG008 all-benchmark region (sensitivity analysis), SNVs and indels combined (Hasan 2026) somatic-hg008-20261011-protocol-all-region-overall Aggregation: Not reported Prospectively frozen external benchmarking reveals benchmark-context dependence in somatic variant calling; AmbioSpire P003/T001 publication source data and reproducibility package v1.0.0 (Zenodo) · Zenodo tables/Table4_HG008_sensitivity_all_region.tsv, row 'Strelka2', column 'F1'
Configuration: Strelka2 2.9.10 (Hasan 2026)	Protocol: HG008 all-benchmark region (sensitivity analysis), SNVs and indels combined, Mutect2, Strelka2, DeepSomatic and ensembles (Hasan 2026 Table 4) Dataset: NIST/GIAB HG008 tumour-normal WGS (HG008-T pancreatic cancer cell line, matched normal), HG008-T draft somatic small-variant benchmark v0.3	6060 False negatives (SNVs and indels, HG008 all-benchmark region) 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 HG008 all-benchmark region (sensitivity analysis), SNVs and indels combined (Hasan 2026) somatic-hg008-20261011-protocol-all-region-overall Aggregation: Not reported Prospectively frozen external benchmarking reveals benchmark-context dependence in somatic variant calling; AmbioSpire P003/T001 publication source data and reproducibility package v1.0.0 (Zenodo) · Zenodo tables/Table4_HG008_sensitivity_all_region.tsv, row 'Strelka2', column 'FN'
Configuration: Strelka2 2.9.10 (Hasan 2026)	Protocol: HG008 all-benchmark region (sensitivity analysis), SNVs and indels combined, Mutect2, Strelka2, DeepSomatic and ensembles (Hasan 2026 Table 4) Dataset: NIST/GIAB HG008 tumour-normal WGS (HG008-T pancreatic cancer cell line, matched normal), HG008-T draft somatic small-variant benchmark v0.3	4480 False positives (SNVs and indels, HG008 all-benchmark region) 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 HG008 all-benchmark region (sensitivity analysis), SNVs and indels combined (Hasan 2026) somatic-hg008-20261011-protocol-all-region-overall Aggregation: Not reported Prospectively frozen external benchmarking reveals benchmark-context dependence in somatic variant calling; AmbioSpire P003/T001 publication source data and reproducibility package v1.0.0 (Zenodo) · Zenodo tables/Table4_HG008_sensitivity_all_region.tsv, row 'Strelka2', column 'FP'
Configuration: Strelka2 2.9.10 (Hasan 2026)	Protocol: HG008 all-benchmark region (sensitivity analysis), SNVs and indels combined, Mutect2, Strelka2, DeepSomatic and ensembles (Hasan 2026 Table 4) Dataset: NIST/GIAB HG008 tumour-normal WGS (HG008-T pancreatic cancer cell line, matched normal), HG008-T draft somatic small-variant benchmark v0.3	0.731 Precision (SNVs and indels, HG008 all-benchmark region) 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 HG008 all-benchmark region (sensitivity analysis), SNVs and indels combined (Hasan 2026) somatic-hg008-20261011-protocol-all-region-overall Aggregation: Not reported Prospectively frozen external benchmarking reveals benchmark-context dependence in somatic variant calling; AmbioSpire P003/T001 publication source data and reproducibility package v1.0.0 (Zenodo) · Zenodo tables/Table4_HG008_sensitivity_all_region.tsv, row 'Strelka2', column 'Precision'
Configuration: Strelka2 2.9.10 (Hasan 2026)	Protocol: HG008 all-benchmark region (sensitivity analysis), SNVs and indels combined, Mutect2, Strelka2, DeepSomatic and ensembles (Hasan 2026 Table 4) Dataset: NIST/GIAB HG008 tumour-normal WGS (HG008-T pancreatic cancer cell line, matched normal), HG008-T draft somatic small-variant benchmark v0.3	0.667 Recall (SNVs and indels, HG008 all-benchmark region) 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 HG008 all-benchmark region (sensitivity analysis), SNVs and indels combined (Hasan 2026) somatic-hg008-20261011-protocol-all-region-overall Aggregation: Not reported Prospectively frozen external benchmarking reveals benchmark-context dependence in somatic variant calling; AmbioSpire P003/T001 publication source data and reproducibility package v1.0.0 (Zenodo) · Zenodo tables/Table4_HG008_sensitivity_all_region.tsv, row 'Strelka2', column 'Recall'
Configuration: Strelka2 2.9.10 (Hasan 2026)	Protocol: HG008 all-benchmark region (sensitivity analysis), SNVs and indels combined, Mutect2, Strelka2, DeepSomatic and ensembles (Hasan 2026 Table 4) Dataset: NIST/GIAB HG008 tumour-normal WGS (HG008-T pancreatic cancer cell line, matched normal), HG008-T draft somatic small-variant benchmark v0.3	12100 True positives (SNVs and indels, HG008 all-benchmark region) 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 HG008 all-benchmark region (sensitivity analysis), SNVs and indels combined (Hasan 2026) somatic-hg008-20261011-protocol-all-region-overall Aggregation: Not reported Prospectively frozen external benchmarking reveals benchmark-context dependence in somatic variant calling; AmbioSpire P003/T001 publication source data and reproducibility package v1.0.0 (Zenodo) · Zenodo tables/Table4_HG008_sensitivity_all_region.tsv, row 'Strelka2', column 'TP'
Configuration: Strelka2 2.9.10 (Hasan 2026)	Protocol: HG008 primary region (nogermlineinterference), indels, Mutect2, Strelka2, DeepSomatic and ensembles (Hasan 2026 Table 2, Class 'INDEL') Dataset: NIST/GIAB HG008 tumour-normal WGS (HG008-T pancreatic cancer cell line, matched normal), HG008-T draft somatic small-variant benchmark v0.3	0.691 F1 (indel only, HG008 primary region) fraction · higher Uncertainty: 95% CI 0.676722 to 0.704489. Genomic block bootstrap over 5-Mb blocks, linear percentile interval; spatial variation within the benchmark region, not between tumours Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Strelka2 on HG008 primary region (nogermlineinterference), indels (Hasan 2026) somatic-hg008-20261011-protocol-primary-indel Aggregation: Not reported Prospectively frozen external benchmarking reveals benchmark-context dependence in somatic variant calling; AmbioSpire P003/T001 publication source data and reproducibility package v1.0.0 (Zenodo) · Zenodo tables/Table2_HG008_variant_class_metrics.tsv, row 'Strelka2', Class 'INDEL', column 'F1'
Configuration: Strelka2 2.9.10 (Hasan 2026)	Protocol: HG008 primary region (nogermlineinterference), indels, Mutect2, Strelka2, DeepSomatic and ensembles (Hasan 2026 Table 2, Class 'INDEL') Dataset: NIST/GIAB HG008 tumour-normal WGS (HG008-T pancreatic cancer cell line, matched normal), HG008-T draft somatic small-variant benchmark v0.3	2070 False negatives (indel only, HG008 primary region) 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 HG008 primary region (nogermlineinterference), indels (Hasan 2026) somatic-hg008-20261011-protocol-primary-indel Aggregation: Not reported Prospectively frozen external benchmarking reveals benchmark-context dependence in somatic variant calling; AmbioSpire P003/T001 publication source data and reproducibility package v1.0.0 (Zenodo) · Zenodo tables/Table2_HG008_variant_class_metrics.tsv, row 'Strelka2', Class 'INDEL', column 'FN'
Configuration: Strelka2 2.9.10 (Hasan 2026)	Protocol: HG008 primary region (nogermlineinterference), indels, Mutect2, Strelka2, DeepSomatic and ensembles (Hasan 2026 Table 2, Class 'INDEL') Dataset: NIST/GIAB HG008 tumour-normal WGS (HG008-T pancreatic cancer cell line, matched normal), HG008-T draft somatic small-variant benchmark v0.3	487 False positives (indel only, HG008 primary region) 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 HG008 primary region (nogermlineinterference), indels (Hasan 2026) somatic-hg008-20261011-protocol-primary-indel Aggregation: Not reported Prospectively frozen external benchmarking reveals benchmark-context dependence in somatic variant calling; AmbioSpire P003/T001 publication source data and reproducibility package v1.0.0 (Zenodo) · Zenodo tables/Table2_HG008_variant_class_metrics.tsv, row 'Strelka2', Class 'INDEL', column 'FP'
Configuration: Strelka2 2.9.10 (Hasan 2026)	Protocol: HG008 primary region (nogermlineinterference), indels, Mutect2, Strelka2, DeepSomatic and ensembles (Hasan 2026 Table 2, Class 'INDEL') Dataset: NIST/GIAB HG008 tumour-normal WGS (HG008-T pancreatic cancer cell line, matched normal), HG008-T draft somatic small-variant benchmark v0.3	0.855 Precision (indel only, HG008 primary region) 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 HG008 primary region (nogermlineinterference), indels (Hasan 2026) somatic-hg008-20261011-protocol-primary-indel Aggregation: Not reported Prospectively frozen external benchmarking reveals benchmark-context dependence in somatic variant calling; AmbioSpire P003/T001 publication source data and reproducibility package v1.0.0 (Zenodo) · Zenodo tables/Table2_HG008_variant_class_metrics.tsv, row 'Strelka2', Class 'INDEL', column 'Precision'
Configuration: Strelka2 2.9.10 (Hasan 2026)	Protocol: HG008 primary region (nogermlineinterference), indels, Mutect2, Strelka2, DeepSomatic and ensembles (Hasan 2026 Table 2, Class 'INDEL') Dataset: NIST/GIAB HG008 tumour-normal WGS (HG008-T pancreatic cancer cell line, matched normal), HG008-T draft somatic small-variant benchmark v0.3	0.58 Recall (indel only, HG008 primary region) 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 HG008 primary region (nogermlineinterference), indels (Hasan 2026) somatic-hg008-20261011-protocol-primary-indel Aggregation: Not reported Prospectively frozen external benchmarking reveals benchmark-context dependence in somatic variant calling; AmbioSpire P003/T001 publication source data and reproducibility package v1.0.0 (Zenodo) · Zenodo tables/Table2_HG008_variant_class_metrics.tsv, row 'Strelka2', Class 'INDEL', column 'Recall'
Configuration: Strelka2 2.9.10 (Hasan 2026)	Protocol: HG008 primary region (nogermlineinterference), indels, Mutect2, Strelka2, DeepSomatic and ensembles (Hasan 2026 Table 2, Class 'INDEL') Dataset: NIST/GIAB HG008 tumour-normal WGS (HG008-T pancreatic cancer cell line, matched normal), HG008-T draft somatic small-variant benchmark v0.3	2860 True positives (indel only, HG008 primary region) 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 HG008 primary region (nogermlineinterference), indels (Hasan 2026) somatic-hg008-20261011-protocol-primary-indel Aggregation: Not reported Prospectively frozen external benchmarking reveals benchmark-context dependence in somatic variant calling; AmbioSpire P003/T001 publication source data and reproducibility package v1.0.0 (Zenodo) · Zenodo tables/Table2_HG008_variant_class_metrics.tsv, row 'Strelka2', Class 'INDEL', column 'TP'
Configuration: Strelka2 2.9.10 (Hasan 2026)	Protocol: HG008 primary region (nogermlineinterference), SNVs and indels combined, Mutect2, Strelka2, DeepSomatic and ensembles (Hasan 2026 Table 1) Dataset: NIST/GIAB HG008 tumour-normal WGS (HG008-T pancreatic cancer cell line, matched normal), HG008-T draft somatic small-variant benchmark v0.3	0.779 F1 (SNVs and indels, HG008 primary region) fraction · higher Uncertainty: 95% CI 0.743518 to 0.807537. Genomic block bootstrap over 5-Mb blocks, linear percentile interval; spatial variation within the benchmark region, not between tumours Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Strelka2 on HG008 primary region (nogermlineinterference), SNVs and indels combined (Hasan 2026) somatic-hg008-20261011-protocol-primary-overall Aggregation: Not reported Prospectively frozen external benchmarking reveals benchmark-context dependence in somatic variant calling; AmbioSpire P003/T001 publication source data and reproducibility package v1.0.0 (Zenodo) · Zenodo tables/Table1_HG008_primary_metrics.tsv, row 'Strelka2', column 'F1'
Configuration: Strelka2 2.9.10 (Hasan 2026)	Protocol: HG008 primary region (nogermlineinterference), SNVs and indels combined, Mutect2, Strelka2, DeepSomatic and ensembles (Hasan 2026 Table 1) Dataset: NIST/GIAB HG008 tumour-normal WGS (HG008-T pancreatic cancer cell line, matched normal), HG008-T draft somatic small-variant benchmark v0.3	2260 False negatives (SNVs and indels, HG008 primary region) 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 HG008 primary region (nogermlineinterference), SNVs and indels combined (Hasan 2026) somatic-hg008-20261011-protocol-primary-overall Aggregation: Not reported Prospectively frozen external benchmarking reveals benchmark-context dependence in somatic variant calling; AmbioSpire P003/T001 publication source data and reproducibility package v1.0.0 (Zenodo) · Zenodo tables/Table1_HG008_primary_metrics.tsv, row 'Strelka2', column 'FN'
Configuration: Strelka2 2.9.10 (Hasan 2026)	Protocol: HG008 primary region (nogermlineinterference), SNVs and indels combined, Mutect2, Strelka2, DeepSomatic and ensembles (Hasan 2026 Table 1) Dataset: NIST/GIAB HG008 tumour-normal WGS (HG008-T pancreatic cancer cell line, matched normal), HG008-T draft somatic small-variant benchmark v0.3	4410 False positives (SNVs and indels, HG008 primary region) 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 HG008 primary region (nogermlineinterference), SNVs and indels combined (Hasan 2026) somatic-hg008-20261011-protocol-primary-overall Aggregation: Not reported Prospectively frozen external benchmarking reveals benchmark-context dependence in somatic variant calling; AmbioSpire P003/T001 publication source data and reproducibility package v1.0.0 (Zenodo) · Zenodo tables/Table1_HG008_primary_metrics.tsv, row 'Strelka2', column 'FP'
Configuration: Strelka2 2.9.10 (Hasan 2026)	Protocol: HG008 primary region (nogermlineinterference), SNVs and indels combined, Mutect2, Strelka2, DeepSomatic and ensembles (Hasan 2026 Table 1) Dataset: NIST/GIAB HG008 tumour-normal WGS (HG008-T pancreatic cancer cell line, matched normal), HG008-T draft somatic small-variant benchmark v0.3	0.727 Precision (SNVs and indels, HG008 primary region) 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 HG008 primary region (nogermlineinterference), SNVs and indels combined (Hasan 2026) somatic-hg008-20261011-protocol-primary-overall Aggregation: Not reported Prospectively frozen external benchmarking reveals benchmark-context dependence in somatic variant calling; AmbioSpire P003/T001 publication source data and reproducibility package v1.0.0 (Zenodo) · Zenodo tables/Table1_HG008_primary_metrics.tsv, row 'Strelka2', column 'Precision'
Configuration: Strelka2 2.9.10 (Hasan 2026)	Protocol: HG008 primary region (nogermlineinterference), SNVs and indels combined, Mutect2, Strelka2, DeepSomatic and ensembles (Hasan 2026 Table 1) Dataset: NIST/GIAB HG008 tumour-normal WGS (HG008-T pancreatic cancer cell line, matched normal), HG008-T draft somatic small-variant benchmark v0.3	0.839 Recall (SNVs and indels, HG008 primary region) 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 HG008 primary region (nogermlineinterference), SNVs and indels combined (Hasan 2026) somatic-hg008-20261011-protocol-primary-overall Aggregation: Not reported Prospectively frozen external benchmarking reveals benchmark-context dependence in somatic variant calling; AmbioSpire P003/T001 publication source data and reproducibility package v1.0.0 (Zenodo) · Zenodo tables/Table1_HG008_primary_metrics.tsv, row 'Strelka2', column 'Recall'
Configuration: Strelka2 2.9.10 (Hasan 2026)	Protocol: HG008 primary region (nogermlineinterference), SNVs and indels combined, Mutect2, Strelka2, DeepSomatic and ensembles (Hasan 2026 Table 1) Dataset: NIST/GIAB HG008 tumour-normal WGS (HG008-T pancreatic cancer cell line, matched normal), HG008-T draft somatic small-variant benchmark v0.3	11800 True positives (SNVs and indels, HG008 primary region) 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 HG008 primary region (nogermlineinterference), SNVs and indels combined (Hasan 2026) somatic-hg008-20261011-protocol-primary-overall Aggregation: Not reported Prospectively frozen external benchmarking reveals benchmark-context dependence in somatic variant calling; AmbioSpire P003/T001 publication source data and reproducibility package v1.0.0 (Zenodo) · Zenodo tables/Table1_HG008_primary_metrics.tsv, row 'Strelka2', column 'TP'
Configuration: Strelka2 2.9.10 (Hasan 2026)	Protocol: HG008 primary region (nogermlineinterference), SNVs, Mutect2, Strelka2, DeepSomatic and ensembles (Hasan 2026 Table 2, Class 'SNV') Dataset: NIST/GIAB HG008 tumour-normal WGS (HG008-T pancreatic cancer cell line, matched normal), HG008-T draft somatic small-variant benchmark v0.3	0.812 F1 (SNV only, HG008 primary region) fraction · higher Uncertainty: 95% CI 0.765275 to 0.850476. Genomic block bootstrap over 5-Mb blocks, linear percentile interval; spatial variation within the benchmark region, not between tumours Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Strelka2 on HG008 primary region (nogermlineinterference), SNVs (Hasan 2026) somatic-hg008-20261011-protocol-primary-snv Aggregation: Not reported Prospectively frozen external benchmarking reveals benchmark-context dependence in somatic variant calling; AmbioSpire P003/T001 publication source data and reproducibility package v1.0.0 (Zenodo) · Zenodo tables/Table2_HG008_variant_class_metrics.tsv, row 'Strelka2', Class 'SNV', column 'F1'
Configuration: Strelka2 2.9.10 (Hasan 2026)	Protocol: HG008 primary region (nogermlineinterference), SNVs, Mutect2, Strelka2, DeepSomatic and ensembles (Hasan 2026 Table 2, Class 'SNV') Dataset: NIST/GIAB HG008 tumour-normal WGS (HG008-T pancreatic cancer cell line, matched normal), HG008-T draft somatic small-variant benchmark v0.3	183 False negatives (SNV only, HG008 primary region) 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 HG008 primary region (nogermlineinterference), SNVs (Hasan 2026) somatic-hg008-20261011-protocol-primary-snv Aggregation: Not reported Prospectively frozen external benchmarking reveals benchmark-context dependence in somatic variant calling; AmbioSpire P003/T001 publication source data and reproducibility package v1.0.0 (Zenodo) · Zenodo tables/Table2_HG008_variant_class_metrics.tsv, row 'Strelka2', Class 'SNV', column 'FN'
Configuration: Strelka2 2.9.10 (Hasan 2026)	Protocol: HG008 primary region (nogermlineinterference), SNVs, Mutect2, Strelka2, DeepSomatic and ensembles (Hasan 2026 Table 2, Class 'SNV') Dataset: NIST/GIAB HG008 tumour-normal WGS (HG008-T pancreatic cancer cell line, matched normal), HG008-T draft somatic small-variant benchmark v0.3	3930 False positives (SNV only, HG008 primary region) 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 HG008 primary region (nogermlineinterference), SNVs (Hasan 2026) somatic-hg008-20261011-protocol-primary-snv Aggregation: Not reported Prospectively frozen external benchmarking reveals benchmark-context dependence in somatic variant calling; AmbioSpire P003/T001 publication source data and reproducibility package v1.0.0 (Zenodo) · Zenodo tables/Table2_HG008_variant_class_metrics.tsv, row 'Strelka2', Class 'SNV', column 'FP'
Configuration: Strelka2 2.9.10 (Hasan 2026)	Protocol: HG008 primary region (nogermlineinterference), SNVs, Mutect2, Strelka2, DeepSomatic and ensembles (Hasan 2026 Table 2, Class 'SNV') Dataset: NIST/GIAB HG008 tumour-normal WGS (HG008-T pancreatic cancer cell line, matched normal), HG008-T draft somatic small-variant benchmark v0.3	0.694 Precision (SNV only, HG008 primary region) 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 HG008 primary region (nogermlineinterference), SNVs (Hasan 2026) somatic-hg008-20261011-protocol-primary-snv Aggregation: Not reported Prospectively frozen external benchmarking reveals benchmark-context dependence in somatic variant calling; AmbioSpire P003/T001 publication source data and reproducibility package v1.0.0 (Zenodo) · Zenodo tables/Table2_HG008_variant_class_metrics.tsv, row 'Strelka2', Class 'SNV', column 'Precision'
Configuration: Strelka2 2.9.10 (Hasan 2026)	Protocol: HG008 primary region (nogermlineinterference), SNVs, Mutect2, Strelka2, DeepSomatic and ensembles (Hasan 2026 Table 2, Class 'SNV') Dataset: NIST/GIAB HG008 tumour-normal WGS (HG008-T pancreatic cancer cell line, matched normal), HG008-T draft somatic small-variant benchmark v0.3	0.98 Recall (SNV only, HG008 primary region) 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 HG008 primary region (nogermlineinterference), SNVs (Hasan 2026) somatic-hg008-20261011-protocol-primary-snv Aggregation: Not reported Prospectively frozen external benchmarking reveals benchmark-context dependence in somatic variant calling; AmbioSpire P003/T001 publication source data and reproducibility package v1.0.0 (Zenodo) · Zenodo tables/Table2_HG008_variant_class_metrics.tsv, row 'Strelka2', Class 'SNV', column 'Recall'
Configuration: Strelka2 2.9.10 (Hasan 2026)	Protocol: HG008 primary region (nogermlineinterference), SNVs, Mutect2, Strelka2, DeepSomatic and ensembles (Hasan 2026 Table 2, Class 'SNV') Dataset: NIST/GIAB HG008 tumour-normal WGS (HG008-T pancreatic cancer cell line, matched normal), HG008-T draft somatic small-variant benchmark v0.3	8900 True positives (SNV only, HG008 primary region) 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 HG008 primary region (nogermlineinterference), SNVs (Hasan 2026) somatic-hg008-20261011-protocol-primary-snv Aggregation: Not reported Prospectively frozen external benchmarking reveals benchmark-context dependence in somatic variant calling; AmbioSpire P003/T001 publication source data and reproducibility package v1.0.0 (Zenodo) · Zenodo tables/Table2_HG008_variant_class_metrics.tsv, row 'Strelka2', Class 'SNV', column 'TP'

Source checking is not independent reproduction. Release 2026-10-22-1b7cf027e4f6.

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Evidence

Source checking verifies the cited claim or transcription. It does not establish independent reproduction.

Evidence table

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Trace each statement to its source and review. A context-only reference supports the record generally; it does not verify an individual field. Source checking does not reproduce an experiment.

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Claims, original sources and review scope · Release 2026-10-22-1b7cf027e4f6
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Release 2026-10-22-1b7cf027e4f6 · Record review: source checked

2 source records and release history

Prospectively frozen external benchmarking reveals benchmark-context dependence in somatic variant calling · Original source · Research Square preprint rs-11210923 version 1, posted 2026-10-05; manuscript PDF (16 pages)
AmbioSpire P003/T001 publication source data and reproducibility package v1.0.0 (Zenodo) · Original source · Zenodo record 22998005, version 1.0.0, published 2026-09-27; file P003-T001-publication-data-v1.0.0-zenodo-final.zip (1,934,562 bytes, md5 a1fdab6108197602f07f72db77d9f996)

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Technical metadata and extraction receipts

Stable ID: somatic-hg008-20261011-config-strelka2

areas: dna-genomes
contexts: clinical_research
method types: conventional_pipeline
reported name: Strelka2
foundation model eligible: false
parameters: quay.io/biocontainers/strelka:2.9.10--h9ee0642_1, digest sha256:e6133fa935d444aaf3aa04b57256a580d9b3498298fc17cb5f4a9818116105ec5; PASS calls
access reuse: Public open-source software
source locator: Online Methods 'Variant callers and retained software identities' and 'Consensus definitions and metrics'; Zenodo metadata/software_versions.tsv
version: 2.9.10
provenance note: Strelka2 as run in the cited HG008 evaluation.

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