Protocol

HG008 primary region (nogermlineinterference), indels, Mutect2, Strelka2, DeepSomatic and ensembles (Hasan 2026 Table 2, Class 'INDEL')

TP, FP, FN, precision, recall and F1 of PASS calls from three callers and three deterministic ensembles: HG008 primary region (nogermlineinterference), indels.

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 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

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	F1 (indel only, HG008 primary region)	False negatives (indel only, HG008 primary region)	False positives (indel only, HG008 primary region)	Precision (indel only, HG008 primary region)	Recall (indel only, HG008 primary region)	True positives (indel only, HG008 primary region)
Mutect2 (GATK 4.6.2.0) (Hasan 2026)Evaluation	0.824 (best in column)	1302	253	0.935	0.736	3634
Union of Mutect2, Strelka2 and DeepSomatic (at least one caller) (Hasan 2026)Evaluation	0.809	1081 (best in column)	740	0.839	0.781 (best in column)	3855 (best in column)
Majority of Mutect2, Strelka2 and DeepSomatic (at least two callers) (Hasan 2026)Evaluation	0.753	1942	26	0.991	0.607	2994
Strelka2 2.9.10 (Hasan 2026)Evaluation	0.691	2074	487	0.855	0.58	2862
DeepSomatic 1.10.0, bundled WGS model (Hasan 2026)Evaluation	0.69	2324	28	0.989	0.529	2612
Strict intersection of Mutect2, Strelka2 and DeepSomatic (all three callers) (Hasan 2026)Evaluation	0.628	2677	2 (best in column)	0.999 (best in column)	0.458	2259

All 36 result rows with coverage, uncertainty and sources

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Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

Applied filters: All linked evaluations

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 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	0.69 F1 (indel only, HG008 primary region) fraction · higher Uncertainty: 95% CI 0.676907 to 0.701908. 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 DeepSomatic 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 'DeepSomatic', Class 'INDEL', column 'F1'
Configuration: DeepSomatic 1.10.0, bundled WGS model (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	2320 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 DeepSomatic 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 'DeepSomatic', Class 'INDEL', column 'FN'
Configuration: DeepSomatic 1.10.0, bundled WGS model (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	28 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 DeepSomatic 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 'DeepSomatic', Class 'INDEL', column 'FP'
Configuration: DeepSomatic 1.10.0, bundled WGS model (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	0.989 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 DeepSomatic 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 'DeepSomatic', Class 'INDEL', column 'Precision'
Configuration: DeepSomatic 1.10.0, bundled WGS model (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	0.529 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 DeepSomatic 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 'DeepSomatic', Class 'INDEL', column 'Recall'
Configuration: DeepSomatic 1.10.0, bundled WGS model (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	2610 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 DeepSomatic 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 'DeepSomatic', Class 'INDEL', column 'TP'
Configuration: Majority of Mutect2, Strelka2 and DeepSomatic (at least two callers) (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	0.753 F1 (indel only, HG008 primary region) fraction · higher Uncertainty: 95% CI 0.740977 to 0.763650. 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	Author-reported evaluation · Source checked Methods, coverage and source Majority 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 'Majority', Class 'INDEL', column 'F1'
Configuration: Majority of Mutect2, Strelka2 and DeepSomatic (at least two callers) (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	1940 False negatives (indel only, HG008 primary 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 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 'Majority', Class 'INDEL', column 'FN'
Configuration: Majority of Mutect2, Strelka2 and DeepSomatic (at least two callers) (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	26 False positives (indel only, HG008 primary 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 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 'Majority', Class 'INDEL', column 'FP'
Configuration: Majority of Mutect2, Strelka2 and DeepSomatic (at least two callers) (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	0.991 Precision (indel only, HG008 primary 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 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 'Majority', Class 'INDEL', column 'Precision'
Configuration: Majority of Mutect2, Strelka2 and DeepSomatic (at least two callers) (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	0.607 Recall (indel only, HG008 primary 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 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 'Majority', Class 'INDEL', column 'Recall'
Configuration: Majority of Mutect2, Strelka2 and DeepSomatic (at least two callers) (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	2990 True positives (indel only, HG008 primary 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 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 'Majority', Class 'INDEL', column 'TP'
Configuration: Mutect2 (GATK 4.6.2.0) (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	0.824 F1 (indel only, HG008 primary region) fraction · higher Uncertainty: 95% CI 0.814022 to 0.833409. 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 Mutect2 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 'Mutect2', Class 'INDEL', column 'F1'
Configuration: Mutect2 (GATK 4.6.2.0) (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	1300 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 Mutect2 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 'Mutect2', Class 'INDEL', column 'FN'
Configuration: Mutect2 (GATK 4.6.2.0) (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	253 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 Mutect2 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 'Mutect2', Class 'INDEL', column 'FP'
Configuration: Mutect2 (GATK 4.6.2.0) (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	0.935 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 Mutect2 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 'Mutect2', Class 'INDEL', column 'Precision'
Configuration: Mutect2 (GATK 4.6.2.0) (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	0.736 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 Mutect2 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 'Mutect2', Class 'INDEL', column 'Recall'
Configuration: Mutect2 (GATK 4.6.2.0) (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	3630 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 Mutect2 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 'Mutect2', Class 'INDEL', 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: Strict intersection of Mutect2, Strelka2 and DeepSomatic (all three callers) (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	0.628 F1 (indel only, HG008 primary region) fraction · higher Uncertainty: 95% CI 0.613363 to 0.641664. 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	Author-reported evaluation · Source checked Methods, coverage and source StrictIntersection 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 'StrictIntersection', Class 'INDEL', column 'F1'

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

Methods and evaluation design

Procedure, tasks and evaluated configurations

Recorded evaluations

Each evaluation records what was tested and under which conditions.

Baseline coverage

Reference methods help show what a model adds beyond simple controls. We track a null control and a conventional method for each protocol.

0 of 2 active baseline roles have published Rewire measurements in this release. Measurements on a selected protocol do not establish coverage of an entire suite.

No execution recipe linked to this protocol. Recipe availability does not establish a completed evaluation.

Author-reported evaluations: 3
External evaluations: 3

Literature evidence is not a Rewire measurement. Executed but unpublished runs and private review status are not included.

Null control

Proposed control: requires review

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Protocol-specific applicability, permitted inputs, access, split, evaluator and execution requirements need review before implementation or execution.

This is a suggested selection rule, not a validated method or a measured score.

Conventional reference

Proposed control: requires review

Select an upstream conventional reference after reviewing the full protocol

Protocol-specific applicability, permitted inputs, access, split, evaluator and execution requirements need review before implementation or execution.

This is a suggested selection rule, not a validated method or a measured score.

Protocol coverage CSV (gzip) · Model evaluation matrix (gzip) · Source table (gzip) · Release and checksums (gzip)

Coverage is derived from release 2026-10-22-1b7cf027e4f6. Source citations describe the original records; they do not validate an unreviewed baseline proposal. No results have been generated by this audit.

Run instructions

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Strengths, limitations and unresolved questions

Evidence

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Evidence table

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Claims, original sources and review scope · Release 2026-10-22-1b7cf027e4f6
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Sources and history

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-protocol-primary-indel

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/Table2_HG008_variant_class_metrics.tsv, Class 'INDEL'
metric: f1-score
denominator: 4936
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.; Intervals are 95% block-bootstrap percentile intervals over 5-Mb genomic blocks (10,000 replicates); they describe spatial variation within this benchmark, not between tumours.; The primary region (nogermlineinterference) holds 14,014 of the 18,207 truth variants in the full benchmark; the rest are sites with germline interference. Over the full benchmark (Table 4) overall F1 is 0.70 to 0.79 rather than 0.78 to 0.91, and in the germline-interference stratum DeepSomatic F1 is 0.0528 (Results).
source locator: Online Methods 'PASS filtering, normalization and exact comparison', 'Consensus definitions and metrics', 'Benchmark regions'; Zenodo tables/Table2_HG008_variant_class_metrics.tsv

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