Configuration

Strict intersection of Mutect2, Strelka2 and DeepSomatic (all three callers) (Hasan 2026)

Strict intersection of Mutect2, Strelka2 and DeepSomatic (all three callers), a configuration of Majority-vote consensus of somatic callers: Variant kept only when all three of Mutect2, Strelka2 and DeepSomatic report it.

4 evaluations · 24 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.

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)
Strict intersection of Mutect2, Strelka2 and DeepSomatic (all three callers) (Hasan 2026)Evaluation	HG008 primary region (nogermlineinterference), indels, Mutect2, Strelka2, DeepSomatic and ensembles (Hasan 2026 Table 2, Class 'INDEL')	0.628	Not reported	Not reported	Not reported	2677	Not reported	Not reported	Not reported	2	Not reported	Not reported	Not reported	0.999	Not reported	Not reported	Not reported	0.458	Not reported	Not reported	Not reported	2259	Not reported	Not reported	Not reported
Strict intersection of Mutect2, Strelka2 and DeepSomatic (all three callers) (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	0.739	Not reported	Not reported	Not reported	7540	Not reported	Not reported	Not reported	7	Not reported	Not reported	Not reported	0.999	Not reported	Not reported	Not reported	0.586	Not reported	Not reported	Not reported	10667	Not reported
Strict intersection of Mutect2, Strelka2 and DeepSomatic (all three callers) (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	0.861	Not reported	Not reported	Not reported	3426	Not reported	Not reported	Not reported	5	Not reported	Not reported	Not reported	1	Not reported	Not reported	Not reported	0.756	Not reported	Not reported	Not reported	10588
Strict intersection of Mutect2, Strelka2 and DeepSomatic (all three callers) (Hasan 2026)Evaluation	HG008 primary region (nogermlineinterference), SNVs, Mutect2, Strelka2, DeepSomatic and ensembles (Hasan 2026 Table 2, Class 'SNV')	Not reported	0.957	Not reported	Not reported	Not reported	749	Not reported	Not reported	Not reported	3	Not reported	Not reported	Not reported	1	Not reported	Not reported	Not reported	0.917	Not reported	Not reported	Not reported	8329	Not reported	Not reported

All 24 result rows with coverage, uncertainty and sources

Filter evaluations

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: 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'
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	7540 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 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 'FN'
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	7 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 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 'FP'
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	0.999 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 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 'Precision'
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	0.586 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 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 'Recall'
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	10700 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 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 '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'
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	2680 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 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 'FN'
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	2 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 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 'FP'
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	0.999 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 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 'Precision'
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	0.458 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 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 'Recall'
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	2260 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 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 'TP'
Configuration: Strict intersection of Mutect2, Strelka2 and DeepSomatic (all three callers) (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	0.861 F1 (SNVs and indels, HG008 primary region) fraction · higher Uncertainty: 95% CI 0.855191 to 0.865782. 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), 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 'StrictIntersection', column 'F1'
Configuration: Strict intersection of Mutect2, Strelka2 and DeepSomatic (all three callers) (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	3430 False negatives (SNVs and indels, 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 StrictIntersection 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 'StrictIntersection', column 'FN'
Configuration: Strict intersection of Mutect2, Strelka2 and DeepSomatic (all three callers) (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	5 False positives (SNVs and indels, 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 StrictIntersection 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 'StrictIntersection', column 'FP'
Configuration: Strict intersection of Mutect2, Strelka2 and DeepSomatic (all three callers) (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	1 Precision (SNVs and indels, 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 StrictIntersection 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 'StrictIntersection', column 'Precision'
Configuration: Strict intersection of Mutect2, Strelka2 and DeepSomatic (all three callers) (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	0.756 Recall (SNVs and indels, 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 StrictIntersection 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 'StrictIntersection', column 'Recall'
Configuration: Strict intersection of Mutect2, Strelka2 and DeepSomatic (all three callers) (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	10600 True positives (SNVs and indels, 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 StrictIntersection 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 'StrictIntersection', column 'TP'
Configuration: Strict intersection of Mutect2, Strelka2 and DeepSomatic (all three callers) (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	0.957 F1 (SNV only, HG008 primary region) fraction · higher Uncertainty: 95% CI 0.952594 to 0.960939. 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), 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 'StrictIntersection', Class 'SNV', column 'F1'
Configuration: Strict intersection of Mutect2, Strelka2 and DeepSomatic (all three callers) (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	749 False negatives (SNV 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 StrictIntersection 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 'StrictIntersection', Class 'SNV', column 'FN'
Configuration: Strict intersection of Mutect2, Strelka2 and DeepSomatic (all three callers) (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	3 False positives (SNV 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 StrictIntersection 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 'StrictIntersection', Class 'SNV', column 'FP'
Configuration: Strict intersection of Mutect2, Strelka2 and DeepSomatic (all three callers) (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	1 Precision (SNV 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 StrictIntersection 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 'StrictIntersection', Class 'SNV', column 'Precision'
Configuration: Strict intersection of Mutect2, Strelka2 and DeepSomatic (all three callers) (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	0.917 Recall (SNV 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 StrictIntersection 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 'StrictIntersection', Class 'SNV', column 'Recall'
Configuration: Strict intersection of Mutect2, Strelka2 and DeepSomatic (all three callers) (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	8330 True positives (SNV 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 StrictIntersection 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 'StrictIntersection', Class 'SNV', column 'TP'

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

areas: dna-genomes
contexts: clinical_research
method types: conventional_pipeline
reported name: StrictIntersection
foundation model eligible: false
parameters: Variant kept only when all three of Mutect2, Strelka2 and DeepSomatic report it
access reuse: Ensemble rule defined in the source; no released implementation (Zenodo archive holds no executable code)
source locator: Online Methods 'Variant callers and retained software identities' and 'Consensus definitions and metrics'; Zenodo metadata/software_versions.tsv
missing metadata: version: reason: inapplicable; note: Deterministic ensemble rule over the three versioned callers
provenance note: StrictIntersection as run in the cited HG008 evaluation.

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