Evaluation

Union on HG008 primary region (nogermlineinterference), SNVs and indels combined (Hasan 2026)

Published comparison transcribed from the pinned source; not reproduced.

Evaluation results

1 evaluation · 6 results. Different protocols are not a single leaderboard.

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

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

Tested configuration	F1 (SNVs and indels, HG008 primary region)	False negatives (SNVs and indels, HG008 primary region)	False positives (SNVs and indels, HG008 primary region)	Precision (SNVs and indels, HG008 primary region)	Recall (SNVs and indels, HG008 primary region)	True positives (SNVs and indels, HG008 primary region)
Union of Mutect2, Strelka2 and DeepSomatic (at least one caller) (Hasan 2026)Evaluation	0.801	1194	5173	0.712	0.915	12820

All 6 result rows with coverage, uncertainty and sources

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: Union of Mutect2, Strelka2 and DeepSomatic (at least one caller) (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	0.801 F1 (SNVs and indels, HG008 primary region) fraction · higher Uncertainty: 95% CI 0.766634 to 0.828861. 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 Union 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 'Union', column 'F1'
Configuration: Union of Mutect2, Strelka2 and DeepSomatic (at least one caller) (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	1190 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 Union 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 'Union', column 'FN'
Configuration: Union of Mutect2, Strelka2 and DeepSomatic (at least one caller) (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	5170 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 Union 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 'Union', column 'FP'
Configuration: Union of Mutect2, Strelka2 and DeepSomatic (at least one caller) (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	0.712 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 Union 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 'Union', column 'Precision'
Configuration: Union of Mutect2, Strelka2 and DeepSomatic (at least one caller) (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	0.915 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 Union 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 'Union', column 'Recall'
Configuration: Union of Mutect2, Strelka2 and DeepSomatic (at least one caller) (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	12800 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 Union 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 'Union', column 'TP'

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

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Release 2026-10-22-1b7cf027e4f6 · Evidence verified: Not verified

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Evaluation procedure

HG008 primary region (nogermlineinterference), SNVs and indels combined, Mutect2, Strelka2, DeepSomatic and ensembles (Hasan 2026 Table 1)

Configuration: Union of Mutect2, Strelka2 and DeepSomatic (at least one caller) (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

origin: Author-reported evaluation
configuration: Primary source as retrieved 2026-10-11
protocol id: somatic-hg008-20261011-protocol-primary-overall
dataset version: HG008-T draft somatic small-variant benchmark v0.3
split: External test; procedure frozen on HCC1395 before HG008 truth access
population: One HG008 tumour-normal pair
inputs: Tumour and matched-normal WGS alignments
adaptation: Not reported
metric implementation: Exact normalised CHROM/POS/REF/ALT match of PASS calls within the region
aggregation: Single pair; 95% block-bootstrap interval on F1
budget: Not reported

Metadata review: source checked. Unreported conditions prevent automatic comparisons.

Reproduction

Split: External test; procedure frozen on HCC1395 before HG008 truth access
Adaptation: Not reported
Scoring implementation: Exact normalised CHROM/POS/REF/ALT match of PASS calls within the region

No execution recipe has been verified for this exact configuration and evaluation. A benchmark's general instructions may use different inputs, splits or model settings.

Reproducing this published result requires matching its model configuration, data, split and scorer. Source checking or a successful smoke test does not establish score reproduction.

Evidence

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Evidence table

Inspect claims, sources and review details

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

36 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
Comparison: adaptation Not reported Context-only references	Prospectively frozen external benchmarking reveals benchmark-context dependence in somatic variant calling Original source ↗ Zenodo tables/Table1_HG008_primary_metrics.tsv, row 'Union' 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	missing or unspecified No individual claim review recorded author reported Audit details Field: `attributes.comparison.adaptation` Source artifact SHA-256: `358502e2394c1f90214889c40aae8b29d2836cddbcf55460688d7fda051dc1c3` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: adaptation Not reported Context-only references	AmbioSpire P003/T001 publication source data and reproducibility package v1.0.0 (Zenodo) Original source ↗ Zenodo tables/Table1_HG008_primary_metrics.tsv, row 'Union' 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	missing or unspecified No individual claim review recorded author reported Audit details Field: `attributes.comparison.adaptation` 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
Comparison: aggregation Single pair; 95% block-bootstrap interval on F1 Context-only references	Prospectively frozen external benchmarking reveals benchmark-context dependence in somatic variant calling Original source ↗ Zenodo tables/Table1_HG008_primary_metrics.tsv, row 'Union' 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 author reported Audit details Field: `attributes.comparison.aggregation` Source artifact SHA-256: `358502e2394c1f90214889c40aae8b29d2836cddbcf55460688d7fda051dc1c3` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: aggregation Single pair; 95% block-bootstrap interval on F1 Context-only references	AmbioSpire P003/T001 publication source data and reproducibility package v1.0.0 (Zenodo) Original source ↗ Zenodo tables/Table1_HG008_primary_metrics.tsv, row 'Union' 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 author reported Audit details Field: `attributes.comparison.aggregation` 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
Comparison: budget Not reported Context-only references	Prospectively frozen external benchmarking reveals benchmark-context dependence in somatic variant calling Original source ↗ Zenodo tables/Table1_HG008_primary_metrics.tsv, row 'Union' 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	missing or unspecified No individual claim review recorded author reported Audit details Field: `attributes.comparison.budget` Source artifact SHA-256: `358502e2394c1f90214889c40aae8b29d2836cddbcf55460688d7fda051dc1c3` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: budget Not reported Context-only references	AmbioSpire P003/T001 publication source data and reproducibility package v1.0.0 (Zenodo) Original source ↗ Zenodo tables/Table1_HG008_primary_metrics.tsv, row 'Union' 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	missing or unspecified No individual claim review recorded author reported Audit details Field: `attributes.comparison.budget` 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
Comparison: dataset version HG008-T draft somatic small-variant benchmark v0.3 Context-only references	Prospectively frozen external benchmarking reveals benchmark-context dependence in somatic variant calling Original source ↗ Zenodo tables/Table1_HG008_primary_metrics.tsv, row 'Union' 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 author reported Audit details Field: `attributes.comparison.dataset_version` Source artifact SHA-256: `358502e2394c1f90214889c40aae8b29d2836cddbcf55460688d7fda051dc1c3` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: dataset version HG008-T draft somatic small-variant benchmark v0.3 Context-only references	AmbioSpire P003/T001 publication source data and reproducibility package v1.0.0 (Zenodo) Original source ↗ Zenodo tables/Table1_HG008_primary_metrics.tsv, row 'Union' 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 author reported Audit details Field: `attributes.comparison.dataset_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
Comparison: inputs Tumour and matched-normal WGS alignments Context-only references	Prospectively frozen external benchmarking reveals benchmark-context dependence in somatic variant calling Original source ↗ Zenodo tables/Table1_HG008_primary_metrics.tsv, row 'Union' 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 author reported Audit details Field: `attributes.comparison.inputs` Source artifact SHA-256: `358502e2394c1f90214889c40aae8b29d2836cddbcf55460688d7fda051dc1c3` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: inputs Tumour and matched-normal WGS alignments Context-only references	AmbioSpire P003/T001 publication source data and reproducibility package v1.0.0 (Zenodo) Original source ↗ Zenodo tables/Table1_HG008_primary_metrics.tsv, row 'Union' 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 author reported Audit details Field: `attributes.comparison.inputs` 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

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Sources and history

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

2 source records and release history

Prospectively frozen external benchmarking reveals benchmark-context dependence in somatic variant calling · Original source · Research Square preprint rs-11210923 version 1, posted 2026-10-05; manuscript PDF (16 pages)
AmbioSpire P003/T001 publication source data and reproducibility package v1.0.0 (Zenodo) · Original source · Zenodo record 22998005, version 1.0.0, published 2026-09-27; file P003-T001-publication-data-v1.0.0-zenodo-final.zip (1,934,562 bytes, md5 a1fdab6108197602f07f72db77d9f996)

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Technical metadata and extraction receipts

Stable ID: somatic-hg008-20261011-eval-union-primary-overall

areas: dna-genomes
contexts: clinical_research
origin: author_reported
protocol: somatic-hg008-20261011-protocol-primary-overall
version: Primary source as retrieved 2026-10-11
comparison: protocol id: somatic-hg008-20261011-protocol-primary-overall; dataset version: HG008-T draft somatic small-variant benchmark v0.3; split: External test; procedure frozen on HCC1395 before HG008 truth access; population: One HG008 tumour-normal pair; inputs: Tumour and matched-normal WGS alignments; adaptation: Not reported; metric implementation: Exact normalised CHROM/POS/REF/ALT match of PASS calls within the region; aggregation: Single pair; 95% block-bootstrap interval on F1; budget: Not reported
source locator: Zenodo tables/Table1_HG008_primary_metrics.tsv, row 'Union'
missing metadata: comparison.adaptation: reason: inapplicable; note: No training or tuning on HG008; comparison.budget: reason: unreported

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