Relevance of HG008 primary region (nogermlineinterference), SNVs (Hasan 2026) to "Select a tumour DNA somatic variant-calling workflow"

Stable ID: use-case-mapping-somatic-hg008-20261011-primary-snv

field

links:assessed_by:somatic-hg008-20261011-protocol-primary-snv

value

somatic-hg008-20261011-protocol-primary-snv

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 primary region (nogermlineinterference), SNVs

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Single-author preprint, not peer reviewed; the author founded AmbioSpire LLC, under which the study was run.; One cell-line tumour-normal pair (HG008) and a draft truth set (HG008-T v0.3,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.; Intervals are 95% block-bootstrap percentile intervals over 5-Mb genomic blocks (10,000 replicates); they describe spatial variation within this benchmark, not between tumours.; The primary region (nogermlineinterference) holds 14,014 of the 18,207 truth variants in the full benchmark; the rest are sites with germline interference. Over the full benchmark (Table 4) overall F1 is 0.70 to 0.79 rather than 0.78 to 0.91, and in the germline-interference stratum DeepSomatic F1 is 0.0528 (Results).

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

SNVs, primary region

stratum order

1

reviewed evaluations

somatic-hg008-20261011-eval-deepsomatic-primary-snv; somatic-hg008-20261011-eval-majority-primary-snv; somatic-hg008-20261011-eval-mutect2-primary-snv; somatic-hg008-20261011-eval-strelka2-primary-snv; somatic-hg008-20261011-eval-strictintersection-primary-snv; somatic-hg008-20261011-eval-union-primary-snv

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

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• subject: Select a tumour DNA somatic variant-calling workflow