SEQC2 HCC1395 tumour-only, indels, AUPRC (Krishnamachari et al. 2026 Supplementary Table 1)
Area under the precision-recall curve for tumour-only calling: SEQC2 HCC1395 tumour-only, indels.
Overview
An explanatory profile has not yet been reviewed for this record.
Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.
9 recorded evaluations, 9 metric rows. A comparison chart has not yet been validated for these results. The table retains the individual findings and their sources.
Results
Results are available, but no reviewed comparison panel is linked in this release.
All evaluations
9 evaluations · 9 results. Different protocols are not a single leaderboard.
Protocol: SEQC2 HCC1395 tumour-only, indels, AUPRC (Krishnamachari et al. 2026 Supplementary Table 1) · Dataset: SEQC2 HCC1395 tumour Illumina HiSeq WGS (WGS_IL_T_1), high-confidence regions
Sorted by AUPRC (indel only, tumour-only) (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.
All 9 result rows with coverage, uncertainty and sources
Filter evaluations
Applied filters: All linked evaluations
Source checking is not independent reproduction. Release 2026-10-22-1b7cf027e4f6.
Methods and evaluation design
Procedure, tasks and evaluated configurations
Recorded evaluations
Each evaluation records what was tested and under which conditions.
- ClairS-TO on seqc2-indel tumour-only (Krishnamachari et al. 2026)
- DeepSom-BLCA on seqc2-indel tumour-only (Krishnamachari et al. 2026)
- DeepSom-ESAD on seqc2-indel tumour-only (Krishnamachari et al. 2026)
- DeepSom-GACA on seqc2-indel tumour-only (Krishnamachari et al. 2026)
- DeepSom-LAML on seqc2-indel tumour-only (Krishnamachari et al. 2026)
- DeepSom-LINC on seqc2-indel tumour-only (Krishnamachari et al. 2026)
- Deepsomatic (tumor-only) on seqc2-indel tumour-only (Krishnamachari et al. 2026)
- Mutect2 (tumor-only) on seqc2-indel tumour-only (Krishnamachari et al. 2026)
- VarNet-T on seqc2-indel tumour-only (Krishnamachari et al. 2026)
Baseline coverage
Reference methods help show what a model adds beyond simple controls. We track a null control and a conventional method for each protocol.
0 of 2 active baseline roles have published Rewire measurements in this release. Measurements on a selected protocol do not establish coverage of an entire suite.
No execution recipe linked to this protocol. Recipe availability does not establish a completed evaluation.
- Author-reported evaluations
- 1
- External evaluations
- 8
Literature evidence is not a Rewire measurement. Executed but unpublished runs and private review status are not included.
Null control
Proposed control: requires review
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Protocol-specific applicability, permitted inputs, access, split, evaluator and execution requirements need review before implementation or execution.
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Conventional reference
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Protocol coverage CSV (gzip) · Model evaluation matrix (gzip) · Source table (gzip) · Release and checksums (gzip)
Coverage is derived from release 2026-10-22-1b7cf027e4f6. Source citations describe the original records; they do not validate an unreviewed baseline proposal. No results have been generated by this audit.
Run instructions
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Strengths, limitations and unresolved questions
Evidence
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Evidence table
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Sources and history
Release 2026-10-22-1b7cf027e4f6 · Record review: source checked
3 source records and release history
- Improved tumor-only variant calling and mutation burden estimation with VarNet-T · Original source · Nature Communications, published 2026-04-09; PMC13243554 full-text XML
- VarNet-T Supplementary Information · Original source · Supplementary Information PDF (41467_2026_71705_MOESM1_ESM.pdf), 28 pages
- VarNet-T Source Data workbook · Original source · Source Data file (41467_2026_71705_MOESM6_ESM.xlsx)
Technical metadata and extraction receipts
Stable ID: somatic-varnet-t-20261011-protocol-seqc2-indel
- areas
- dna-genomes
- contexts
- clinical_research
- protocol
- Tumour BAM only; each caller's score (VarNet-T score, Mutect2 TLOD, DeepSomatic QUAL, DeepSom cnn_score, ClairS-TO QUAL) is varied to trace a precision-recall curve against the truth set; AUPRC reported.
- version
- Supplementary Table 1, column SEQC2 INDEL
- metric
- auprc
- limitations
- Developer paper: the authors developed VarNet-T (and earlier VarNet); its rows are author_reported. Comparators were run by the authors.; Tumour-only calling: the matched normal was used only to build the truth sets, not by the callers.; Only AUPRC is extracted; the threshold-optimised best F1 values are shown in figures only.; No interval estimates.; DeepSomatic's models were trained on SEQC2 data (Introduction), so its SEQC2 row is not held out.; DeepSom's developers describe it as a caller of somatic SNVs (github.com/sergeyvilov/DeepSom repository description, checked 2026-10-11; not a pinned source); this source prints indel AUPRC for its models without explanation.
- source locator
- Supplementary Table 1, column SEQC2 INDEL; Methods 'Implementation of tumor-only variant callers' and 'Performance metrics'
Related records
- uses data: SEQC2 HCC1395 tumour Illumina HiSeq WGS (WGS_IL_T_1), high-confidence regions
- assessment: ClairS-TO on seqc2-indel tumour-only (Krishnamachari et al. 2026)
- assessment: DeepSom-BLCA on seqc2-indel tumour-only (Krishnamachari et al. 2026)
- assessment: DeepSom-ESAD on seqc2-indel tumour-only (Krishnamachari et al. 2026)
- assessment: DeepSom-GACA on seqc2-indel tumour-only (Krishnamachari et al. 2026)
- assessment: DeepSom-LAML on seqc2-indel tumour-only (Krishnamachari et al. 2026)
- assessment: DeepSom-LINC on seqc2-indel tumour-only (Krishnamachari et al. 2026)
- assessment: Deepsomatic (tumor-only) on seqc2-indel tumour-only (Krishnamachari et al. 2026)
- assessment: Mutect2 (tumor-only) on seqc2-indel tumour-only (Krishnamachari et al. 2026)
- assessment: VarNet-T on seqc2-indel tumour-only (Krishnamachari et al. 2026)
- assessed by: Select a tumour DNA somatic variant-calling workflow