Dataset

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

Matched tumour-normal whole-genome data for the GIAB HG008 cancer cell line and its draft clonal/truncal somatic small-variant truth set, as used by Hasan 2026.

Evaluation results

24 evaluations · 144 results. Different protocols are not a single leaderboard.

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: DeepSomatic 1.10.0, bundled WGS model (Hasan 2026)	Protocol: HG008 all-benchmark region (sensitivity analysis), SNVs and indels combined, Mutect2, Strelka2, DeepSomatic and ensembles (Hasan 2026 Table 4) Dataset: NIST/GIAB HG008 tumour-normal WGS (HG008-T pancreatic cancer cell line, matched normal), HG008-T draft somatic small-variant benchmark v0.3	0.776 F1 (SNVs and indels, HG008 all-benchmark region) fraction · higher Uncertainty: 95% CI 0.7689 to 0.7822. Genomic block bootstrap over 5-Mb blocks, linear percentile interval; prespecified, but executed after the primary external evaluation; spatial variation within the benchmark region, not between tumours Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DeepSomatic on HG008 all-benchmark region (sensitivity analysis), SNVs and indels combined (Hasan 2026) somatic-hg008-20261011-protocol-all-region-overall Aggregation: Not reported Prospectively frozen external benchmarking reveals benchmark-context dependence in somatic variant calling; AmbioSpire P003/T001 publication source data and reproducibility package v1.0.0 (Zenodo) · Zenodo tables/Table4_HG008_sensitivity_all_region.tsv, row 'DeepSomatic', column 'F1'
Configuration: DeepSomatic 1.10.0, bundled WGS model (Hasan 2026)	Protocol: HG008 all-benchmark region (sensitivity analysis), SNVs and indels combined, Mutect2, Strelka2, DeepSomatic and ensembles (Hasan 2026 Table 4) Dataset: NIST/GIAB HG008 tumour-normal WGS (HG008-T pancreatic cancer cell line, matched normal), HG008-T draft somatic small-variant benchmark v0.3	6590 False negatives (SNVs and indels, HG008 all-benchmark region) count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DeepSomatic on HG008 all-benchmark region (sensitivity analysis), SNVs and indels combined (Hasan 2026) somatic-hg008-20261011-protocol-all-region-overall Aggregation: Not reported Prospectively frozen external benchmarking reveals benchmark-context dependence in somatic variant calling; AmbioSpire P003/T001 publication source data and reproducibility package v1.0.0 (Zenodo) · Zenodo tables/Table4_HG008_sensitivity_all_region.tsv, row 'DeepSomatic', column 'FN'
Configuration: DeepSomatic 1.10.0, bundled WGS model (Hasan 2026)	Protocol: HG008 all-benchmark region (sensitivity analysis), SNVs and indels combined, Mutect2, Strelka2, DeepSomatic and ensembles (Hasan 2026 Table 4) Dataset: NIST/GIAB HG008 tumour-normal WGS (HG008-T pancreatic cancer cell line, matched normal), HG008-T draft somatic small-variant benchmark v0.3	133 False positives (SNVs and indels, HG008 all-benchmark region) count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DeepSomatic on HG008 all-benchmark region (sensitivity analysis), SNVs and indels combined (Hasan 2026) somatic-hg008-20261011-protocol-all-region-overall Aggregation: Not reported Prospectively frozen external benchmarking reveals benchmark-context dependence in somatic variant calling; AmbioSpire P003/T001 publication source data and reproducibility package v1.0.0 (Zenodo) · Zenodo tables/Table4_HG008_sensitivity_all_region.tsv, row 'DeepSomatic', column 'FP'
Configuration: DeepSomatic 1.10.0, bundled WGS model (Hasan 2026)	Protocol: HG008 all-benchmark region (sensitivity analysis), SNVs and indels combined, Mutect2, Strelka2, DeepSomatic and ensembles (Hasan 2026 Table 4) Dataset: NIST/GIAB HG008 tumour-normal WGS (HG008-T pancreatic cancer cell line, matched normal), HG008-T draft somatic small-variant benchmark v0.3	0.989 Precision (SNVs and indels, HG008 all-benchmark region) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DeepSomatic on HG008 all-benchmark region (sensitivity analysis), SNVs and indels combined (Hasan 2026) somatic-hg008-20261011-protocol-all-region-overall Aggregation: Not reported Prospectively frozen external benchmarking reveals benchmark-context dependence in somatic variant calling; AmbioSpire P003/T001 publication source data and reproducibility package v1.0.0 (Zenodo) · Zenodo tables/Table4_HG008_sensitivity_all_region.tsv, row 'DeepSomatic', column 'Precision'
Configuration: DeepSomatic 1.10.0, bundled WGS model (Hasan 2026)	Protocol: HG008 all-benchmark region (sensitivity analysis), SNVs and indels combined, Mutect2, Strelka2, DeepSomatic and ensembles (Hasan 2026 Table 4) Dataset: NIST/GIAB HG008 tumour-normal WGS (HG008-T pancreatic cancer cell line, matched normal), HG008-T draft somatic small-variant benchmark v0.3	0.638 Recall (SNVs and indels, HG008 all-benchmark region) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DeepSomatic on HG008 all-benchmark region (sensitivity analysis), SNVs and indels combined (Hasan 2026) somatic-hg008-20261011-protocol-all-region-overall Aggregation: Not reported Prospectively frozen external benchmarking reveals benchmark-context dependence in somatic variant calling; AmbioSpire P003/T001 publication source data and reproducibility package v1.0.0 (Zenodo) · Zenodo tables/Table4_HG008_sensitivity_all_region.tsv, row 'DeepSomatic', column 'Recall'
Configuration: DeepSomatic 1.10.0, bundled WGS model (Hasan 2026)	Protocol: HG008 all-benchmark region (sensitivity analysis), SNVs and indels combined, Mutect2, Strelka2, DeepSomatic and ensembles (Hasan 2026 Table 4) Dataset: NIST/GIAB HG008 tumour-normal WGS (HG008-T pancreatic cancer cell line, matched normal), HG008-T draft somatic small-variant benchmark v0.3	11600 True positives (SNVs and indels, HG008 all-benchmark region) count · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DeepSomatic on HG008 all-benchmark region (sensitivity analysis), SNVs and indels combined (Hasan 2026) somatic-hg008-20261011-protocol-all-region-overall Aggregation: Not reported Prospectively frozen external benchmarking reveals benchmark-context dependence in somatic variant calling; AmbioSpire P003/T001 publication source data and reproducibility package v1.0.0 (Zenodo) · Zenodo tables/Table4_HG008_sensitivity_all_region.tsv, row 'DeepSomatic', column 'TP'
Configuration: 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: DeepSomatic 1.10.0, bundled WGS model (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	0.897 F1 (SNVs and indels, HG008 primary region) fraction · higher Uncertainty: 95% CI 0.892866 to 0.901452. 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), 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 'DeepSomatic', column 'F1'
Configuration: DeepSomatic 1.10.0, bundled WGS model (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	2510 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 DeepSomatic 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 'DeepSomatic', column 'FN'
Configuration: DeepSomatic 1.10.0, bundled WGS model (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	124 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 DeepSomatic 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 'DeepSomatic', column 'FP'
Configuration: DeepSomatic 1.10.0, bundled WGS model (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	0.989 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 DeepSomatic 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 'DeepSomatic', column 'Precision'
Configuration: DeepSomatic 1.10.0, bundled WGS model (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	0.821 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 DeepSomatic 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 'DeepSomatic', column 'Recall'
Configuration: DeepSomatic 1.10.0, bundled WGS model (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	11500 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 DeepSomatic 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 'DeepSomatic', column 'TP'
Configuration: DeepSomatic 1.10.0, bundled WGS model (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	0.984 F1 (SNV only, HG008 primary region) fraction · higher Uncertainty: 95% CI 0.982090 to 0.986558. 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), 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 'DeepSomatic', Class 'SNV', column 'F1'
Configuration: DeepSomatic 1.10.0, bundled WGS model (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	186 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 DeepSomatic 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 'DeepSomatic', Class 'SNV', column 'FN'
Configuration: DeepSomatic 1.10.0, bundled WGS model (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	96 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 DeepSomatic 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 'DeepSomatic', Class 'SNV', column 'FP'
Configuration: DeepSomatic 1.10.0, bundled WGS model (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	0.989 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 DeepSomatic 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 'DeepSomatic', Class 'SNV', column 'Precision'
Configuration: DeepSomatic 1.10.0, bundled WGS model (Hasan 2026)	Protocol: HG008 primary region (nogermlineinterference), SNVs, Mutect2, Strelka2, DeepSomatic and ensembles (Hasan 2026 Table 2, Class 'SNV') Dataset: NIST/GIAB HG008 tumour-normal WGS (HG008-T pancreatic cancer cell line, matched normal), HG008-T draft somatic small-variant benchmark v0.3	0.98 Recall (SNV only, HG008 primary region) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DeepSomatic 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 'DeepSomatic', Class 'SNV', column 'Recall'
Configuration: DeepSomatic 1.10.0, bundled WGS model (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	8890 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 DeepSomatic 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 'DeepSomatic', Class 'SNV', column 'TP'
Configuration: Majority of Mutect2, Strelka2 and DeepSomatic (at least two callers) (Hasan 2026)	Protocol: HG008 all-benchmark region (sensitivity analysis), SNVs and indels combined, Mutect2, Strelka2, DeepSomatic and ensembles (Hasan 2026 Table 4) Dataset: NIST/GIAB HG008 tumour-normal WGS (HG008-T pancreatic cancer cell line, matched normal), HG008-T draft somatic small-variant benchmark v0.3	0.794 F1 (SNVs and indels, HG008 all-benchmark region) fraction · higher Uncertainty: 95% CI 0.7875 to 0.8003. Genomic block bootstrap over 5-Mb blocks, linear percentile interval; prespecified, but executed after the primary external evaluation; spatial variation within the benchmark region, not between tumours Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Majority on HG008 all-benchmark region (sensitivity analysis), SNVs and indels combined (Hasan 2026) somatic-hg008-20261011-protocol-all-region-overall Aggregation: Not reported Prospectively frozen external benchmarking reveals benchmark-context dependence in somatic variant calling; AmbioSpire P003/T001 publication source data and reproducibility package v1.0.0 (Zenodo) · Zenodo tables/Table4_HG008_sensitivity_all_region.tsv, row 'Majority', column 'F1'

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One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.

14 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-10-22-1b7cf027e4f6
Property and statement	Original source and location	Review and provenance
Assay Tumour-normal WGS (platform, read length and coverage not stated) aligned with BWA-MEM2 v2.3 to GRCh38_GIABv3_no_alt_analysis_set_maskedGRC_decoys_MAP2K3_KMT2C_KCNJ18 Context-only references	Prospectively frozen external benchmarking reveals benchmark-context dependence in somatic variant calling Original source ↗ Online Methods 'Development and external resources', 'Reference and alignment', 'Benchmark regions'; Results 'Caller and deterministic-consensus performance'; Zenodo metadata/benchmark_resource_identities.tsv Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Research Square preprint rs-11210923 version 1, posted 2026-10-05; manuscript PDF (16 pages) Retrieved: 2026-10-11T21:39:12Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.assay` Source artifact SHA-256: `358502e2394c1f90214889c40aae8b29d2836cddbcf55460688d7fda051dc1c3` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Assay Tumour-normal WGS (platform, read length and coverage not stated) aligned with BWA-MEM2 v2.3 to GRCh38_GIABv3_no_alt_analysis_set_maskedGRC_decoys_MAP2K3_KMT2C_KCNJ18 Context-only references	AmbioSpire P003/T001 publication source data and reproducibility package v1.0.0 (Zenodo) Original source ↗ Online Methods 'Development and external resources', 'Reference and alignment', 'Benchmark regions'; Results 'Caller and deterministic-consensus performance'; Zenodo metadata/benchmark_resource_identities.tsv Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 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) Retrieved: 2026-10-11T21:39:34Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.assay` Source artifact SHA-256: `629921b1198f4a5290d191857d13f98e54a1d132d722caf0ac83805f7e24a40d` Hash scope: SHA-256 of the downloaded zip. Member SHA-256 values for the extracted tables: tables/Table1_HG008_primary_metrics.tsv df3ac2809164be08676c9a010d3c7324ca08998a4b3964d5fb0c7a2201445fd6; tables/Table2_HG008_variant_class_metrics.tsv 6fe473217eda2e9b87c5291d28ff6e14339107b1b88346a6f72e62473713ed4a; tables/Table4_HG008_sensitivity_all_region.tsv f838cab270034cc351c5fa0fd7442b7ca6318beca598640b988eaa3952123ef8 (each equals the archive's own SHA256SUMS entry). Inspected artifact
Population One tumour-normal pair (HG008-T and matched normal). Primary region 'nogermlineinterference': 14,014 truth variants (9,078 SNVs, 4,936 indels). Region 'all': 18,207 truth variants (TP + FN in Table 4). Context-only references	Prospectively frozen external benchmarking reveals benchmark-context dependence in somatic variant calling Original source ↗ Online Methods 'Development and external resources', 'Reference and alignment', 'Benchmark regions'; Results 'Caller and deterministic-consensus performance'; Zenodo metadata/benchmark_resource_identities.tsv Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Research Square preprint rs-11210923 version 1, posted 2026-10-05; manuscript PDF (16 pages) Retrieved: 2026-10-11T21:39:12Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.population` Source artifact SHA-256: `358502e2394c1f90214889c40aae8b29d2836cddbcf55460688d7fda051dc1c3` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Population One tumour-normal pair (HG008-T and matched normal). Primary region 'nogermlineinterference': 14,014 truth variants (9,078 SNVs, 4,936 indels). Region 'all': 18,207 truth variants (TP + FN in Table 4). Context-only references	AmbioSpire P003/T001 publication source data and reproducibility package v1.0.0 (Zenodo) Original source ↗ Online Methods 'Development and external resources', 'Reference and alignment', 'Benchmark regions'; Results 'Caller and deterministic-consensus performance'; Zenodo metadata/benchmark_resource_identities.tsv Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 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) Retrieved: 2026-10-11T21:39:34Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.population` Source artifact SHA-256: `629921b1198f4a5290d191857d13f98e54a1d132d722caf0ac83805f7e24a40d` Hash scope: SHA-256 of the downloaded zip. Member SHA-256 values for the extracted tables: tables/Table1_HG008_primary_metrics.tsv df3ac2809164be08676c9a010d3c7324ca08998a4b3964d5fb0c7a2201445fd6; tables/Table2_HG008_variant_class_metrics.tsv 6fe473217eda2e9b87c5291d28ff6e14339107b1b88346a6f72e62473713ed4a; tables/Table4_HG008_sensitivity_all_region.tsv f838cab270034cc351c5fa0fd7442b7ca6318beca598640b988eaa3952123ef8 (each equals the archive's own SHA256SUMS entry). Inspected artifact
Source location Online Methods 'Development and external resources', 'Reference and alignment', 'Benchmark regions'; Results 'Caller and deterministic-consensus performance'; Zenodo metadata/benchmark_resource_identities.tsv Context-only references	Prospectively frozen external benchmarking reveals benchmark-context dependence in somatic variant calling Original source ↗ Online Methods 'Development and external resources', 'Reference and alignment', 'Benchmark regions'; Results 'Caller and deterministic-consensus performance'; Zenodo metadata/benchmark_resource_identities.tsv Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Research Square preprint rs-11210923 version 1, posted 2026-10-05; manuscript PDF (16 pages) Retrieved: 2026-10-11T21:39:12Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.source_locator` Source artifact SHA-256: `358502e2394c1f90214889c40aae8b29d2836cddbcf55460688d7fda051dc1c3` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Source location Online Methods 'Development and external resources', 'Reference and alignment', 'Benchmark regions'; Results 'Caller and deterministic-consensus performance'; Zenodo metadata/benchmark_resource_identities.tsv Context-only references	AmbioSpire P003/T001 publication source data and reproducibility package v1.0.0 (Zenodo) Original source ↗ Online Methods 'Development and external resources', 'Reference and alignment', 'Benchmark regions'; Results 'Caller and deterministic-consensus performance'; Zenodo metadata/benchmark_resource_identities.tsv Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 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) Retrieved: 2026-10-11T21:39:34Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.source_locator` Source artifact SHA-256: `629921b1198f4a5290d191857d13f98e54a1d132d722caf0ac83805f7e24a40d` Hash scope: SHA-256 of the downloaded zip. Member SHA-256 values for the extracted tables: tables/Table1_HG008_primary_metrics.tsv df3ac2809164be08676c9a010d3c7324ca08998a4b3964d5fb0c7a2201445fd6; tables/Table2_HG008_variant_class_metrics.tsv 6fe473217eda2e9b87c5291d28ff6e14339107b1b88346a6f72e62473713ed4a; tables/Table4_HG008_sensitivity_all_region.tsv f838cab270034cc351c5fa0fd7442b7ca6318beca598640b988eaa3952123ef8 (each equals the archive's own SHA256SUMS entry). Inspected artifact
Split External test only: the procedure was developed on SEQC2 HCC1395/HCC1395BL (v1.2.1) and frozen before HG008 truth access. Context-only references	Prospectively frozen external benchmarking reveals benchmark-context dependence in somatic variant calling Original source ↗ Online Methods 'Development and external resources', 'Reference and alignment', 'Benchmark regions'; Results 'Caller and deterministic-consensus performance'; Zenodo metadata/benchmark_resource_identities.tsv Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Research Square preprint rs-11210923 version 1, posted 2026-10-05; manuscript PDF (16 pages) Retrieved: 2026-10-11T21:39:12Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.split` Source artifact SHA-256: `358502e2394c1f90214889c40aae8b29d2836cddbcf55460688d7fda051dc1c3` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Split External test only: the procedure was developed on SEQC2 HCC1395/HCC1395BL (v1.2.1) and frozen before HG008 truth access. Context-only references	AmbioSpire P003/T001 publication source data and reproducibility package v1.0.0 (Zenodo) Original source ↗ Online Methods 'Development and external resources', 'Reference and alignment', 'Benchmark regions'; Results 'Caller and deterministic-consensus performance'; Zenodo metadata/benchmark_resource_identities.tsv Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 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) Retrieved: 2026-10-11T21:39:34Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.split` Source artifact SHA-256: `629921b1198f4a5290d191857d13f98e54a1d132d722caf0ac83805f7e24a40d` Hash scope: SHA-256 of the downloaded zip. Member SHA-256 values for the extracted tables: tables/Table1_HG008_primary_metrics.tsv df3ac2809164be08676c9a010d3c7324ca08998a4b3964d5fb0c7a2201445fd6; tables/Table2_HG008_variant_class_metrics.tsv 6fe473217eda2e9b87c5291d28ff6e14339107b1b88346a6f72e62473713ed4a; tables/Table4_HG008_sensitivity_all_region.tsv f838cab270034cc351c5fa0fd7442b7ca6318beca598640b988eaa3952123ef8 (each equals the archive's own SHA256SUMS entry). Inspected artifact
Version NIST_HG008-T_somatic-smvar_DraftBenchmark_V0.3-20260425 (truth VCF SHA-256 6ff5b215e0dc634c85da6164cffbd5790233258fcc48c88a598331430b061cad) Context-only references	Prospectively frozen external benchmarking reveals benchmark-context dependence in somatic variant calling Original source ↗ Online Methods 'Development and external resources', 'Reference and alignment', 'Benchmark regions'; Results 'Caller and deterministic-consensus performance'; Zenodo metadata/benchmark_resource_identities.tsv Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Research Square preprint rs-11210923 version 1, posted 2026-10-05; manuscript PDF (16 pages) Retrieved: 2026-10-11T21:39:12Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.version` Source artifact SHA-256: `358502e2394c1f90214889c40aae8b29d2836cddbcf55460688d7fda051dc1c3` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Version NIST_HG008-T_somatic-smvar_DraftBenchmark_V0.3-20260425 (truth VCF SHA-256 6ff5b215e0dc634c85da6164cffbd5790233258fcc48c88a598331430b061cad) Context-only references	AmbioSpire P003/T001 publication source data and reproducibility package v1.0.0 (Zenodo) Original source ↗ Online Methods 'Development and external resources', 'Reference and alignment', 'Benchmark regions'; Results 'Caller and deterministic-consensus performance'; Zenodo metadata/benchmark_resource_identities.tsv Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 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) Retrieved: 2026-10-11T21:39:34Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.version` Source artifact SHA-256: `629921b1198f4a5290d191857d13f98e54a1d132d722caf0ac83805f7e24a40d` Hash scope: SHA-256 of the downloaded zip. Member SHA-256 values for the extracted tables: tables/Table1_HG008_primary_metrics.tsv df3ac2809164be08676c9a010d3c7324ca08998a4b3964d5fb0c7a2201445fd6; tables/Table2_HG008_variant_class_metrics.tsv 6fe473217eda2e9b87c5291d28ff6e14339107b1b88346a6f72e62473713ed4a; tables/Table4_HG008_sensitivity_all_region.tsv f838cab270034cc351c5fa0fd7442b7ca6318beca598640b988eaa3952123ef8 (each equals the archive's own SHA256SUMS entry). Inspected artifact

How to read the evidence

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-data-hg008-wgs

areas: dna-genomes
contexts: clinical_research
version: NIST_HG008-T_somatic-smvar_DraftBenchmark_V0.3-20260425 (truth VCF SHA-256 6ff5b215e0dc634c85da6164cffbd5790233258fcc48c88a598331430b061cad)
population: One tumour-normal pair (HG008-T and matched normal). Primary region 'nogermlineinterference': 14,014 truth variants (9,078 SNVs, 4,936 indels). Region 'all': 18,207 truth variants (TP + FN in Table 4).
split: External test only: the procedure was developed on SEQC2 HCC1395/HCC1395BL (v1.2.1) and frozen before HG008 truth access.
assay: Tumour-normal WGS (platform, read length and coverage not stated) aligned with BWA-MEM2 v2.3 to GRCh38_GIABv3_no_alt_analysis_set_maskedGRC_decoys_MAP2K3_KMT2C_KCNJ18
source locator: Online Methods 'Development and external resources', 'Reference and alignment', 'Benchmark regions'; Results 'Caller and deterministic-consensus performance'; Zenodo metadata/benchmark_resource_identities.tsv
missing metadata: accession: reason: unreported; note: Read accessions for HG008 are not given; truth and BED bytes are protected and not redistributed

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