Protocol

HG008 all-benchmark region (sensitivity analysis), SNVs and indels combined, Mutect2, Strelka2, DeepSomatic and ensembles (Hasan 2026 Table 4)

TP, FP, FN, precision, recall and F1 of PASS calls from three callers and three deterministic ensembles: HG008 all-benchmark region (sensitivity analysis), SNVs and indels combined.

6 evaluations · 36 results

Overview

An explanatory profile has not yet been reviewed for this record.

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

6 recorded evaluations, 36 metric rows. A comparison chart has not yet been validated for these results. The table retains the individual findings and their sources.

View coverage and remaining gaps across all benchmarks

Results

Results are available, but no reviewed comparison panel is linked in this release.

All evaluations

6 evaluations · 36 results. Different protocols are not a single leaderboard.

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

Sorted by F1 (SNVs and indels, HG008 all-benchmark 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	F1 (SNVs and indels, HG008 all-benchmark region)	False negatives (SNVs and indels, HG008 all-benchmark region)	False positives (SNVs and indels, HG008 all-benchmark region)	Precision (SNVs and indels, HG008 all-benchmark region)	Recall (SNVs and indels, HG008 all-benchmark region)	True positives (SNVs and indels, HG008 all-benchmark region)
Majority of Mutect2, Strelka2 and DeepSomatic (at least two callers) (Hasan 2026)Evaluation	0.794 (best in column)	6138	126	0.99	0.663	12069
Mutect2 (GATK 4.6.2.0) (Hasan 2026)Evaluation	0.792	5738	822	0.938	0.685	12469
DeepSomatic 1.10.0, bundled WGS model (Hasan 2026)Evaluation	0.776	6589	133	0.989	0.638	11618
Strict intersection of Mutect2, Strelka2 and DeepSomatic (all three callers) (Hasan 2026)Evaluation	0.739	7540	7 (best in column)	0.999 (best in column)	0.586	10667
Union of Mutect2, Strelka2 and DeepSomatic (at least one caller) (Hasan 2026)Evaluation	0.73	4707 (best in column)	5297	0.718	0.741 (best in column)	13500 (best in column)
Strelka2 2.9.10 (Hasan 2026)Evaluation	0.698	6058	4475	0.731	0.667	12149

All 36 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: DeepSomatic 1.10.0, bundled WGS model (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	0.776 F1 (SNVs and indels, HG008 all-benchmark region) fraction · higher Uncertainty: 95% CI 0.7689 to 0.7822. 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 DeepSomatic 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 'DeepSomatic', column 'F1'
Configuration: DeepSomatic 1.10.0, bundled WGS model (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	6590 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 DeepSomatic 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 'DeepSomatic', column 'FN'
Configuration: DeepSomatic 1.10.0, bundled WGS model (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	133 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 DeepSomatic 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 'DeepSomatic', column 'FP'
Configuration: DeepSomatic 1.10.0, bundled WGS model (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	0.989 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 DeepSomatic 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 'DeepSomatic', column 'Precision'
Configuration: DeepSomatic 1.10.0, bundled WGS model (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	0.638 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 DeepSomatic 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 'DeepSomatic', column 'Recall'
Configuration: DeepSomatic 1.10.0, bundled WGS model (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	11600 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 DeepSomatic 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 'DeepSomatic', column 'TP'
Configuration: Majority of Mutect2, Strelka2 and DeepSomatic (at least two callers) (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	0.794 F1 (SNVs and indels, HG008 all-benchmark region) fraction · higher Uncertainty: 95% CI 0.7875 to 0.8003. 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	Author-reported evaluation · Source checked Methods, coverage and source Majority 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 'Majority', column 'F1'
Configuration: Majority of Mutect2, Strelka2 and DeepSomatic (at least two callers) (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	6140 False negatives (SNVs and indels, HG008 all-benchmark region) count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Majority 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 'Majority', column 'FN'
Configuration: Majority of Mutect2, Strelka2 and DeepSomatic (at least two callers) (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	126 False positives (SNVs and indels, HG008 all-benchmark region) count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Majority 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 'Majority', column 'FP'
Configuration: Majority of Mutect2, Strelka2 and DeepSomatic (at least two callers) (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	0.99 Precision (SNVs and indels, HG008 all-benchmark region) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Majority 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 'Majority', column 'Precision'
Configuration: Majority of Mutect2, Strelka2 and DeepSomatic (at least two callers) (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	0.663 Recall (SNVs and indels, HG008 all-benchmark region) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Majority 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 'Majority', column 'Recall'
Configuration: Majority of Mutect2, Strelka2 and DeepSomatic (at least two callers) (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	Author-reported evaluation · Source checked Methods, coverage and source Majority 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 'Majority', column 'TP'
Configuration: Mutect2 (GATK 4.6.2.0) (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	0.792 F1 (SNVs and indels, HG008 all-benchmark region) fraction · higher Uncertainty: 95% CI 0.7854 to 0.7980. 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 Mutect2 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 'Mutect2', column 'F1'
Configuration: Mutect2 (GATK 4.6.2.0) (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	5740 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 Mutect2 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 'Mutect2', column 'FN'
Configuration: Mutect2 (GATK 4.6.2.0) (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	822 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 Mutect2 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 'Mutect2', column 'FP'
Configuration: Mutect2 (GATK 4.6.2.0) (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	0.938 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 Mutect2 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 'Mutect2', column 'Precision'
Configuration: Mutect2 (GATK 4.6.2.0) (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	0.685 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 Mutect2 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 'Mutect2', column 'Recall'
Configuration: Mutect2 (GATK 4.6.2.0) (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	12500 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 Mutect2 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 'Mutect2', column 'TP'
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: Strict intersection of Mutect2, Strelka2 and DeepSomatic (all three callers) (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	0.739 F1 (SNVs and indels, HG008 all-benchmark region) fraction · higher Uncertainty: 95% CI 0.7316 to 0.7456. 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	Author-reported evaluation · Source checked Methods, coverage and source StrictIntersection 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 'StrictIntersection', column 'F1'

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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-protocol-all-region-overall

areas: dna-genomes
contexts: clinical_research
protocol: Tumour-normal calling with each caller; PASS calls restricted, split, left-normalised and deduplicated (bcftools 1.20); exact CHROM/POS/REF/ALT match to the truth VCF within the benchmark region. Precision TP/(TP+FP), recall TP/(TP+FN), F1 their harmonic mean. Ensembles: union (at least one caller), majority (at least two), strict intersection (all three).
version: Zenodo v1.0.0 tables/Table4_HG008_sensitivity_all_region.tsv
metric: f1-score
denominator: 18207
limitations: Single-author preprint, not peer reviewed; the author founded AmbioSpire LLC, under which the study was run.; One cell-line tumour-normal pair (HG008) and a draft truth set (HG008-T v0.3, clonal/truncal variants only).; Matching is exact CHROM/POS/REF/ALT after normalisation; no representation-aware comparison, so complex indels may count as errors.; The author does not establish that DeepSomatic's bundled WGS model was trained independently of HCC1395/SEQC2; HG008 itself is described as external to the study's development.; Exact caller command lines and runtime flags were not retained; versions and container digests are.; Union, majority and strict intersection are the author's ensembles (author_reported); the individual callers were run, not developed, by the author.; The original scoring and bootstrap code was not retained; the author reports that a later internal reimplementation reproduced the numbers. No external replication.; Whether DeepSomatic 1.10.0's bundled WGS model was trained with HG008 data is stated neither in the source nor in the DeepSomatic README, metrics page and WGS case study (github.com/google/deepsomatic, commit 09d605a966e5dcb10361cd036e05cb79d21b0062, checked 2026-10-11); the DeepSomatic paper was not checked.; Prespecified sensitivity region that includes variants near germline variants. Its 95% block-bootstrap F1 intervals are printed in the manuscript Results (Supplementary Table 2); that analysis was prespecified but executed after the primary external evaluation.
source locator: Online Methods 'PASS filtering, normalization and exact comparison', 'Consensus definitions and metrics', 'Benchmark regions'; Zenodo tables/Table4_HG008_sensitivity_all_region.tsv

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