Configuration

Mutect2 (GATK 4.6.2.0) (Hasan 2026)

Mutect2 (GATK 4.6.2.0): broadinstitute/gatk:4.6.2.0, digest sha256:71b17ee42d149e8ec112603f5305c873ab60d93949ef8bb62a4fff85427f56fb4; tumour-normal mode; PASS calls.

4 evaluations · 24 results

Overview

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

Evaluations and results

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

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

Sorted by F1 (indel only, HG008 primary region) (higher is better). The best value in each column is highlighted. Decimals are rounded for display; each value links to the printed value and its source.

Tested configuration	Protocol and dataset	F1 (indel only, HG008 primary region)	F1 (SNV only, HG008 primary region)	F1 (SNVs and indels, HG008 all-benchmark region)	F1 (SNVs and indels, HG008 primary region)	False negatives (indel only, HG008 primary region)	False negatives (SNV only, HG008 primary region)	False negatives (SNVs and indels, HG008 all-benchmark region)	False negatives (SNVs and indels, HG008 primary region)	False positives (indel only, HG008 primary region)	False positives (SNV only, HG008 primary region)	False positives (SNVs and indels, HG008 all-benchmark region)	False positives (SNVs and indels, HG008 primary region)	Precision (indel only, HG008 primary region)	Precision (SNV only, HG008 primary region)	Precision (SNVs and indels, HG008 all-benchmark region)	Precision (SNVs and indels, HG008 primary region)	Recall (indel only, HG008 primary region)	Recall (SNV only, HG008 primary region)	Recall (SNVs and indels, HG008 all-benchmark region)	Recall (SNVs and indels, HG008 primary region)	True positives (indel only, HG008 primary region)	True positives (SNV only, HG008 primary region)	True positives (SNVs and indels, HG008 all-benchmark region)	True positives (SNVs and indels, HG008 primary region)
Mutect2 (GATK 4.6.2.0) (Hasan 2026)Evaluation	HG008 primary region (nogermlineinterference), indels, Mutect2, Strelka2, DeepSomatic and ensembles (Hasan 2026 Table 2, Class 'INDEL')	0.824	Not reported	Not reported	Not reported	1302	Not reported	Not reported	Not reported	253	Not reported	Not reported	Not reported	0.935	Not reported	Not reported	Not reported	0.736	Not reported	Not reported	Not reported	3634	Not reported	Not reported	Not reported
Mutect2 (GATK 4.6.2.0) (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	0.792	Not reported	Not reported	Not reported	5738	Not reported	Not reported	Not reported	822	Not reported	Not reported	Not reported	0.938	Not reported	Not reported	Not reported	0.685	Not reported	Not reported	Not reported	12469	Not reported
Mutect2 (GATK 4.6.2.0) (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	0.898	Not reported	Not reported	Not reported	1987	Not reported	Not reported	Not reported	752	Not reported	Not reported	Not reported	0.941	Not reported	Not reported	Not reported	0.858	Not reported	Not reported	Not reported	12027
Mutect2 (GATK 4.6.2.0) (Hasan 2026)Evaluation	HG008 primary region (nogermlineinterference), SNVs, Mutect2, Strelka2, DeepSomatic and ensembles (Hasan 2026 Table 2, Class 'SNV')	Not reported	0.945	Not reported	Not reported	Not reported	685	Not reported	Not reported	Not reported	290	Not reported	Not reported	Not reported	0.967	Not reported	Not reported	Not reported	0.925	Not reported	Not reported	Not reported	8393	Not reported	Not reported

All 24 result rows with coverage, uncertainty and sources

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Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: 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: 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: Mutect2 (GATK 4.6.2.0) (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	0.898 F1 (SNVs and indels, HG008 primary region) fraction · higher Uncertainty: 95% CI 0.892741 to 0.902792. 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), 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 'Mutect2', column 'F1'
Configuration: Mutect2 (GATK 4.6.2.0) (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	1990 False negatives (SNVs and indels, HG008 primary region) count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Mutect2 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 'Mutect2', column 'FN'
Configuration: Mutect2 (GATK 4.6.2.0) (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	752 False positives (SNVs and indels, HG008 primary region) count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Mutect2 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 'Mutect2', column 'FP'
Configuration: Mutect2 (GATK 4.6.2.0) (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	0.941 Precision (SNVs and indels, HG008 primary region) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Mutect2 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 'Mutect2', column 'Precision'
Configuration: Mutect2 (GATK 4.6.2.0) (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	0.858 Recall (SNVs and indels, HG008 primary region) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Mutect2 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 'Mutect2', column 'Recall'
Configuration: Mutect2 (GATK 4.6.2.0) (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	12000 True positives (SNVs and indels, HG008 primary region) count · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Mutect2 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 'Mutect2', column 'TP'
Configuration: Mutect2 (GATK 4.6.2.0) (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	0.945 F1 (SNV only, HG008 primary region) fraction · higher Uncertainty: 95% CI 0.940174 to 0.949952. 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), 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 'Mutect2', Class 'SNV', column 'F1'
Configuration: Mutect2 (GATK 4.6.2.0) (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	685 False negatives (SNV only, HG008 primary region) count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Mutect2 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 'Mutect2', Class 'SNV', column 'FN'
Configuration: Mutect2 (GATK 4.6.2.0) (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	290 False positives (SNV only, HG008 primary region) count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Mutect2 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 'Mutect2', Class 'SNV', column 'FP'
Configuration: Mutect2 (GATK 4.6.2.0) (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	0.967 Precision (SNV only, HG008 primary region) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Mutect2 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 'Mutect2', Class 'SNV', column 'Precision'
Configuration: Mutect2 (GATK 4.6.2.0) (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	0.925 Recall (SNV only, HG008 primary region) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Mutect2 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 'Mutect2', Class 'SNV', column 'Recall'
Configuration: Mutect2 (GATK 4.6.2.0) (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	8390 True positives (SNV only, HG008 primary region) count · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Mutect2 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 'Mutect2', Class 'SNV', column 'TP'

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Release 2026-10-22-1b7cf027e4f6 · Record review: source checked

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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-mutect2

areas: dna-genomes
contexts: clinical_research
method types: conventional_pipeline
reported name: Mutect2
foundation model eligible: false
parameters: broadinstitute/gatk:4.6.2.0, digest sha256:71b17ee42d149e8ec112603f5305c873ab60d93949ef8bb62a4fff85427f56fb4; tumour-normal mode; PASS calls
access reuse: Public open-source software
source locator: Online Methods 'Variant callers and retained software identities' and 'Consensus definitions and metrics'; Zenodo metadata/software_versions.tsv
version: GATK 4.6.2.0
provenance note: Mutect2 as run in the cited HG008 evaluation.

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