Evidence claim

Relevance of HG008 all-benchmark region (sensitivity analysis), SNVs and indels combined (Hasan 2026) to "Select a tumour DNA somatic variant-calling workflow"

Use case: Select a tumour DNA somatic variant-calling workflow
Assessed by: HG008 all-benchmark region (sensitivity analysis), SNVs and indels combined, Mutect2, Strelka2, DeepSomatic and ensembles (Hasan 2026 Table 4)
Relevance: Direct evidence
Endpoint: TP, FP, FN, precision, recall and F1 (with block-bootstrap interval where printed) of Mutect2, Strelka2, DeepSomatic and three ensembles on HG008 all-benchmark region (sensitivity analysis), SNVs and indels combined

A real tumour-normal cell-line pair with a NIST draft truth set, scored by someone who developed none of the callers, measures exactly the per-caller precision, recall and F1 the use case asks for, and adds the HG008 benchmark that the use case lists as a gap.

6 reviewed evaluations

Evidence

Source checking verifies the cited claim or transcription. It does not establish independent reproduction.

Evidence table

Inspect claims, sources and review details

Trace each statement to its source and review. A context-only reference supports the record generally; it does not verify an individual field. Source checking does not reproduce an experiment.

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

38 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
Citation locations 2 values source id somatic-hg008-20261011-source-hasan2026 locator Results 'Caller and deterministic-consensus performance differ in the HG008 external benchmark'; Online Methods; Declarations source id somatic-hg008-20261011-source-hasan2026-zenodo locator tables/Table1_HG008_primary_metrics.tsv, Table2_HG008_variant_class_metrics.tsv, Table4_HG008_sensitivity_all_region.tsv Context-only references	Prospectively frozen external benchmarking reveals benchmark-context dependence in somatic variant calling Original source ↗ somatic-hg008-20261011-source-hasan2026: Results 'Caller and deterministic-consensus performance differ in the HG008 external benchmark'; Online Methods; Declarations; somatic-hg008-20261011-source-hasan2026-zenodo: tables/Table1_HG008_primary_metrics.tsv, Table2_HG008_variant_class_metrics.tsv, Table4_HG008_sensitivity_all_region.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.citation_locators` Source artifact SHA-256: `358502e2394c1f90214889c40aae8b29d2836cddbcf55460688d7fda051dc1c3` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Citation locations 2 values source id somatic-hg008-20261011-source-hasan2026 locator Results 'Caller and deterministic-consensus performance differ in the HG008 external benchmark'; Online Methods; Declarations source id somatic-hg008-20261011-source-hasan2026-zenodo locator tables/Table1_HG008_primary_metrics.tsv, Table2_HG008_variant_class_metrics.tsv, Table4_HG008_sensitivity_all_region.tsv Context-only references	AmbioSpire P003/T001 publication source data and reproducibility package v1.0.0 (Zenodo) Original source ↗ somatic-hg008-20261011-source-hasan2026: Results 'Caller and deterministic-consensus performance differ in the HG008 external benchmark'; Online Methods; Declarations; somatic-hg008-20261011-source-hasan2026-zenodo: tables/Table1_HG008_primary_metrics.tsv, Table2_HG008_variant_class_metrics.tsv, Table4_HG008_sensitivity_all_region.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.citation_locators` 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 group hasan2026-hg008 Context-only references	Prospectively frozen external benchmarking reveals benchmark-context dependence in somatic variant calling Original source ↗ somatic-hg008-20261011-source-hasan2026: Results 'Caller and deterministic-consensus performance differ in the HG008 external benchmark'; Online Methods; Declarations; somatic-hg008-20261011-source-hasan2026-zenodo: tables/Table1_HG008_primary_metrics.tsv, Table2_HG008_variant_class_metrics.tsv, Table4_HG008_sensitivity_all_region.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.comparison_group` Source artifact SHA-256: `358502e2394c1f90214889c40aae8b29d2836cddbcf55460688d7fda051dc1c3` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison group hasan2026-hg008 Context-only references	AmbioSpire P003/T001 publication source data and reproducibility package v1.0.0 (Zenodo) Original source ↗ somatic-hg008-20261011-source-hasan2026: Results 'Caller and deterministic-consensus performance differ in the HG008 external benchmark'; Online Methods; Declarations; somatic-hg008-20261011-source-hasan2026-zenodo: tables/Table1_HG008_primary_metrics.tsv, Table2_HG008_variant_class_metrics.tsv, Table4_HG008_sensitivity_all_region.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.comparison_group` 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 title Mutect2, Strelka2, DeepSomatic and ensembles on HG008 (Hasan 2026) Context-only references	Prospectively frozen external benchmarking reveals benchmark-context dependence in somatic variant calling Original source ↗ somatic-hg008-20261011-source-hasan2026: Results 'Caller and deterministic-consensus performance differ in the HG008 external benchmark'; Online Methods; Declarations; somatic-hg008-20261011-source-hasan2026-zenodo: tables/Table1_HG008_primary_metrics.tsv, Table2_HG008_variant_class_metrics.tsv, Table4_HG008_sensitivity_all_region.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.comparison_title` Source artifact SHA-256: `358502e2394c1f90214889c40aae8b29d2836cddbcf55460688d7fda051dc1c3` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison title Mutect2, Strelka2, DeepSomatic and ensembles on HG008 (Hasan 2026) Context-only references	AmbioSpire P003/T001 publication source data and reproducibility package v1.0.0 (Zenodo) Original source ↗ somatic-hg008-20261011-source-hasan2026: Results 'Caller and deterministic-consensus performance differ in the HG008 external benchmark'; Online Methods; Declarations; somatic-hg008-20261011-source-hasan2026-zenodo: tables/Table1_HG008_primary_metrics.tsv, Table2_HG008_variant_class_metrics.tsv, Table4_HG008_sensitivity_all_region.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.comparison_title` 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
Constraints 2 values Inspect every linked evaluation's source locator before citing a result. Do not combine this mapping's evaluations with any other protocol's results; truth sets, specimens, sequencing and caller versions differ between sources. Context-only references	Prospectively frozen external benchmarking reveals benchmark-context dependence in somatic variant calling Original source ↗ somatic-hg008-20261011-source-hasan2026: Results 'Caller and deterministic-consensus performance differ in the HG008 external benchmark'; Online Methods; Declarations; somatic-hg008-20261011-source-hasan2026-zenodo: tables/Table1_HG008_primary_metrics.tsv, Table2_HG008_variant_class_metrics.tsv, Table4_HG008_sensitivity_all_region.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.constraints` Source artifact SHA-256: `358502e2394c1f90214889c40aae8b29d2836cddbcf55460688d7fda051dc1c3` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Constraints 2 values Inspect every linked evaluation's source locator before citing a result. Do not combine this mapping's evaluations with any other protocol's results; truth sets, specimens, sequencing and caller versions differ between sources. Context-only references	AmbioSpire P003/T001 publication source data and reproducibility package v1.0.0 (Zenodo) Original source ↗ somatic-hg008-20261011-source-hasan2026: Results 'Caller and deterministic-consensus performance differ in the HG008 external benchmark'; Online Methods; Declarations; somatic-hg008-20261011-source-hasan2026-zenodo: tables/Table1_HG008_primary_metrics.tsv, Table2_HG008_variant_class_metrics.tsv, Table4_HG008_sensitivity_all_region.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.constraints` 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
Endpoint TP, FP, FN, precision, recall and F1 (with block-bootstrap interval where printed) of Mutect2, Strelka2, DeepSomatic and three ensembles on HG008 all-benchmark region (sensitivity analysis), SNVs and indels combined Context-only references	Prospectively frozen external benchmarking reveals benchmark-context dependence in somatic variant calling Original source ↗ somatic-hg008-20261011-source-hasan2026: Results 'Caller and deterministic-consensus performance differ in the HG008 external benchmark'; Online Methods; Declarations; somatic-hg008-20261011-source-hasan2026-zenodo: tables/Table1_HG008_primary_metrics.tsv, Table2_HG008_variant_class_metrics.tsv, Table4_HG008_sensitivity_all_region.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.endpoint` Source artifact SHA-256: `358502e2394c1f90214889c40aae8b29d2836cddbcf55460688d7fda051dc1c3` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Endpoint TP, FP, FN, precision, recall and F1 (with block-bootstrap interval where printed) of Mutect2, Strelka2, DeepSomatic and three ensembles on HG008 all-benchmark region (sensitivity analysis), SNVs and indels combined Context-only references	AmbioSpire P003/T001 publication source data and reproducibility package v1.0.0 (Zenodo) Original source ↗ somatic-hg008-20261011-source-hasan2026: Results 'Caller and deterministic-consensus performance differ in the HG008 external benchmark'; Online Methods; Declarations; somatic-hg008-20261011-source-hasan2026-zenodo: tables/Table1_HG008_primary_metrics.tsv, Table2_HG008_variant_class_metrics.tsv, Table4_HG008_sensitivity_all_region.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.endpoint` 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: use-case-mapping-somatic-hg008-20261011-all-region-overall

field: links:assessed_by:somatic-hg008-20261011-protocol-all-region-overall
value: somatic-hg008-20261011-protocol-all-region-overall
relevance: direct
endpoint: TP, FP, FN, precision, recall and F1 (with block-bootstrap interval where printed) of Mutect2, Strelka2, DeepSomatic and three ensembles on HG008 all-benchmark region (sensitivity analysis), SNVs and indels combined
rationale: A real tumour-normal cell-line pair with a NIST draft truth set, scored by someone who developed none of the callers, measures exactly the per-caller precision, recall and F1 the use case asks for, and adds the HG008 benchmark that the use case lists as a gap.
constraints: Inspect every linked evaluation's source locator before citing a result.; Do not combine this mapping's evaluations with any other protocol's results; truth sets, specimens, sequencing and caller versions differ between sources.
limitations: Single-author preprint, not peer reviewed; the author founded AmbioSpire LLC, under which the study was run.; One cell-line tumour-normal pair (HG008) and a draft truth set (HG008-T v0.3, clonal/truncal variants only).; Matching is exact CHROM/POS/REF/ALT after normalisation; no representation-aware comparison, so complex indels may count as errors.; The author does not establish that DeepSomatic's bundled WGS model was trained independently of HCC1395/SEQC2; HG008 itself is described as external to the study's development.; Exact caller command lines and runtime flags were not retained; versions and container digests are.; Union, majority and strict intersection are the author's ensembles (author_reported); the individual callers were run, not developed, by the author.; The original scoring and bootstrap code was not retained; the author reports that a later internal reimplementation reproduced the numbers. No external replication.; Whether DeepSomatic 1.10.0's bundled WGS model was trained with HG008 data is stated neither in the source nor in the DeepSomatic README, metrics page and WGS case study (github.com/google/deepsomatic, commit 09d605a966e5dcb10361cd036e05cb79d21b0062, checked 2026-10-11); the DeepSomatic paper was not checked.; Prespecified sensitivity region that includes variants near germline variants. Its 95% block-bootstrap F1 intervals are printed in the manuscript Results (Supplementary Table 2); that analysis was prespecified but executed after the primary external evaluation.
citation locators: source id: somatic-hg008-20261011-source-hasan2026; locator: Results 'Caller and deterministic-consensus performance differ in the HG008 external benchmark'; Online Methods; Declarations; source id: somatic-hg008-20261011-source-hasan2026-zenodo; locator: tables/Table1_HG008_primary_metrics.tsv, Table2_HG008_variant_class_metrics.tsv, Table4_HG008_sensitivity_all_region.tsv
source locator: somatic-hg008-20261011-source-hasan2026: Results 'Caller and deterministic-consensus performance differ in the HG008 external benchmark'; Online Methods; Declarations; somatic-hg008-20261011-source-hasan2026-zenodo: tables/Table1_HG008_primary_metrics.tsv, Table2_HG008_variant_class_metrics.tsv, Table4_HG008_sensitivity_all_region.tsv
headline metric: f1-score
reason: Add a relevance judgement from the 2026-10-11 oncology use-case literature pass.
comparison group: hasan2026-hg008
comparison title: Mutect2, Strelka2, DeepSomatic and ensembles on HG008 (Hasan 2026)
stratum label: All small variants, all-benchmark region
stratum order: 4
reviewed evaluations: somatic-hg008-20261011-eval-deepsomatic-all-region-overall; somatic-hg008-20261011-eval-majority-all-region-overall; somatic-hg008-20261011-eval-mutect2-all-region-overall; somatic-hg008-20261011-eval-strelka2-all-region-overall; somatic-hg008-20261011-eval-strictintersection-all-region-overall; somatic-hg008-20261011-eval-union-all-region-overall
review: method: ai-assisted-source-review; scope-review; method note: Reviewer checked the endpoint against the use case's inputs and output, the relevance rating and the limitations; every evaluation on the protocol had its values checked in the batch review. Corrections listed in review.md were applied by the extractor.; reviewer: claude; reviewer note: Claude research agent reviewer-onc-1, independent of the extractor uc-oncology; no human review claimed; reviewed at: 2026-10-11T23:30:00Z; note: Automated review; not human scientific review. See docs/reviews/use-cases/tumour-dna-somatic-variant-detection-2026-10-11.md.
pins: record id: somatic-hg008-20261011-eval-deepsomatic-all-region-overall; fields: status; links; attributes.origin; attributes.comparison; sha256: 3657d79f062afc97ef7f47987dc10035098e9591a27731133d2c2b712fddaa2b; record id: somatic-hg008-20261011-eval-majority-all-region-overall; fields: status; links; attributes.origin; attributes.comparison; sha256: c7536604634d37d5a942b19d3ed4a58f9fe48e5a5f5d21051905360a1f92e654; record id: somatic-hg008-20261011-eval-mutect2-all-region-overall; fields: status; links; attributes.origin; attributes.comparison; sha256: fd6f07c62b469fce477cd846b57bfc37a888e8e70348776e742f47eb5e472b1b; record id: somatic-hg008-20261011-eval-strelka2-all-region-overall; fields: status; links; attributes.origin; attributes.comparison; sha256: 9067c68a5a6c5368c2792f4750c2af3cffdfa10fe5f006d7f5b7f26b8aac94ae; record id: somatic-hg008-20261011-eval-strictintersection-all-region-overall; fields: status; links; attributes.origin; attributes.comparison; sha256: 727a9fc456b6af501d4674ea052f8600d619cfa6135cf0371b5f3955c4827a87; 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subject: Select a tumour DNA somatic variant-calling workflow

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