Configuration

Pisces v5.3.0, tumour-only, Illumina (Chen et al. 2025)

Pisces v5.3.0, tumour-only, Illumina: Tumour-only run with the authors' recommended settings.

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.

Evaluations and results

2 evaluations · 14 results. Different protocols are not a single leaderboard.

Dataset: COLO829 tumour Illumina NovaSeq 6000 WGS (ClairS-TO benchmark)

Sorted by AUPRC (indel only, tumour-only, 50x tumour coverage) (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	Protocol and dataset	AUPRC (indel only, tumour-only, 50x tumour coverage)	AUPRC (SNV only, tumour-only, 50x tumour coverage)	F1 (indel only, tumour-only, 50x tumour coverage, at the best-F1 threshold)	F1 (SNV only, tumour-only, 50x tumour coverage, at the best-F1 threshold)	False negatives (indel only, tumour-only, 50x tumour coverage, at the best-F1 threshold)	False negatives (SNV only, tumour-only, 50x tumour coverage, at the best-F1 threshold)	False positives (indel only, tumour-only, 50x tumour coverage, at the best-F1 threshold)	False positives (SNV only, tumour-only, 50x tumour coverage, at the best-F1 threshold)	Precision (indel only, tumour-only, 50x tumour coverage, at the best-F1 threshold)	Precision (SNV only, tumour-only, 50x tumour coverage, at the best-F1 threshold)	Recall (indel only, tumour-only, 50x tumour coverage, at the best-F1 threshold)	Recall (SNV only, tumour-only, 50x tumour coverage, at the best-F1 threshold)	True positives (indel only, tumour-only, 50x tumour coverage, at the best-F1 threshold)	True positives (SNV only, tumour-only, 50x tumour coverage, at the best-F1 threshold)
Pisces v5.3.0, tumour-only, Illumina (Chen et al. 2025)Evaluation	Illumina COLO829 tumour-only, 50x, somatic indels (Chen et al. 2025 Supplementary Table 7b)	0.0008	Not reported	0.003	Not reported	291	Not reported	282,328	Not reported	0.0015	Not reported	0.593	Not reported	424	Not reported
Pisces v5.3.0, tumour-only, Illumina (Chen et al. 2025)Evaluation	Illumina COLO829 tumour-only, 50x, somatic SNVs (Chen et al. 2025 Supplementary Table 7b)	Not reported	0.0635	Not reported	0.224	Not reported	6,085	Not reported	230,502	Not reported	0.129	Not reported	0.849	Not reported	34,145

All 14 result rows with coverage, uncertainty and sources

Filter evaluations

Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

Applied filters: All linked evaluations

Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: Pisces v5.3.0, tumour-only, Illumina (Chen et al. 2025)	Protocol: Illumina COLO829 tumour-only, 50x, somatic indels (Chen et al. 2025 Supplementary Table 7b) Dataset: COLO829 tumour Illumina NovaSeq 6000 WGS (ClairS-TO benchmark)	0.0008 AUPRC (indel only, tumour-only, 50x tumour coverage) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Pisces on illumina-colo829 tumour-only Indel (Chen et al. 2025) somatic-clairs-to-20261011-protocol-illumina-colo829-indel Aggregation: Not reported ClairS-TO: a deep-learning method for long-read tumor-only somatic small variant calling; ClairS-TO Supplementary Information (Supplementary Tables 1-8 and command lines); ClairS-TO Source Data workbook · Supplementary Table 7b, Dataset 'COLO829', Caller 'Pisces', Tumor coverage '50x', Type 'Indel', column 'AUPRC'
Configuration: Pisces v5.3.0, tumour-only, Illumina (Chen et al. 2025)	Protocol: Illumina COLO829 tumour-only, 50x, somatic indels (Chen et al. 2025 Supplementary Table 7b) Dataset: COLO829 tumour Illumina NovaSeq 6000 WGS (ClairS-TO benchmark)	0.003 F1 (indel only, tumour-only, 50x tumour coverage, at the best-F1 threshold) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Pisces on illumina-colo829 tumour-only Indel (Chen et al. 2025) somatic-clairs-to-20261011-protocol-illumina-colo829-indel Aggregation: Not reported ClairS-TO: a deep-learning method for long-read tumor-only somatic small variant calling; ClairS-TO Supplementary Information (Supplementary Tables 1-8 and command lines); ClairS-TO Source Data workbook · Supplementary Table 7b, Dataset 'COLO829', Caller 'Pisces', Tumor coverage '50x', Type 'Indel', column 'F1-score'
Configuration: Pisces v5.3.0, tumour-only, Illumina (Chen et al. 2025)	Protocol: Illumina COLO829 tumour-only, 50x, somatic indels (Chen et al. 2025 Supplementary Table 7b) Dataset: COLO829 tumour Illumina NovaSeq 6000 WGS (ClairS-TO benchmark)	291 False negatives (indel only, tumour-only, 50x tumour coverage, at the best-F1 threshold) count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Pisces on illumina-colo829 tumour-only Indel (Chen et al. 2025) somatic-clairs-to-20261011-protocol-illumina-colo829-indel Aggregation: Not reported ClairS-TO: a deep-learning method for long-read tumor-only somatic small variant calling; ClairS-TO Supplementary Information (Supplementary Tables 1-8 and command lines); ClairS-TO Source Data workbook · Supplementary Table 7b, Dataset 'COLO829', Caller 'Pisces', Tumor coverage '50x', Type 'Indel', column 'FN'
Configuration: Pisces v5.3.0, tumour-only, Illumina (Chen et al. 2025)	Protocol: Illumina COLO829 tumour-only, 50x, somatic indels (Chen et al. 2025 Supplementary Table 7b) Dataset: COLO829 tumour Illumina NovaSeq 6000 WGS (ClairS-TO benchmark)	282,328 False positives (indel only, tumour-only, 50x tumour coverage, at the best-F1 threshold) count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Pisces on illumina-colo829 tumour-only Indel (Chen et al. 2025) somatic-clairs-to-20261011-protocol-illumina-colo829-indel Aggregation: Not reported ClairS-TO: a deep-learning method for long-read tumor-only somatic small variant calling; ClairS-TO Supplementary Information (Supplementary Tables 1-8 and command lines); ClairS-TO Source Data workbook · Supplementary Table 7b, Dataset 'COLO829', Caller 'Pisces', Tumor coverage '50x', Type 'Indel', column 'FP'
Configuration: Pisces v5.3.0, tumour-only, Illumina (Chen et al. 2025)	Protocol: Illumina COLO829 tumour-only, 50x, somatic indels (Chen et al. 2025 Supplementary Table 7b) Dataset: COLO829 tumour Illumina NovaSeq 6000 WGS (ClairS-TO benchmark)	0.0015 Precision (indel only, tumour-only, 50x tumour coverage, at the best-F1 threshold) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Pisces on illumina-colo829 tumour-only Indel (Chen et al. 2025) somatic-clairs-to-20261011-protocol-illumina-colo829-indel Aggregation: Not reported ClairS-TO: a deep-learning method for long-read tumor-only somatic small variant calling; ClairS-TO Supplementary Information (Supplementary Tables 1-8 and command lines); ClairS-TO Source Data workbook · Supplementary Table 7b, Dataset 'COLO829', Caller 'Pisces', Tumor coverage '50x', Type 'Indel', column 'Precision'
Configuration: Pisces v5.3.0, tumour-only, Illumina (Chen et al. 2025)	Protocol: Illumina COLO829 tumour-only, 50x, somatic indels (Chen et al. 2025 Supplementary Table 7b) Dataset: COLO829 tumour Illumina NovaSeq 6000 WGS (ClairS-TO benchmark)	0.593 Recall (indel only, tumour-only, 50x tumour coverage, at the best-F1 threshold) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Pisces on illumina-colo829 tumour-only Indel (Chen et al. 2025) somatic-clairs-to-20261011-protocol-illumina-colo829-indel Aggregation: Not reported ClairS-TO: a deep-learning method for long-read tumor-only somatic small variant calling; ClairS-TO Supplementary Information (Supplementary Tables 1-8 and command lines); ClairS-TO Source Data workbook · Supplementary Table 7b, Dataset 'COLO829', Caller 'Pisces', Tumor coverage '50x', Type 'Indel', column 'Recall'
Configuration: Pisces v5.3.0, tumour-only, Illumina (Chen et al. 2025)	Protocol: Illumina COLO829 tumour-only, 50x, somatic indels (Chen et al. 2025 Supplementary Table 7b) Dataset: COLO829 tumour Illumina NovaSeq 6000 WGS (ClairS-TO benchmark)	424 True positives (indel only, tumour-only, 50x tumour coverage, at the best-F1 threshold) count · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Pisces on illumina-colo829 tumour-only Indel (Chen et al. 2025) somatic-clairs-to-20261011-protocol-illumina-colo829-indel Aggregation: Not reported ClairS-TO: a deep-learning method for long-read tumor-only somatic small variant calling; ClairS-TO Supplementary Information (Supplementary Tables 1-8 and command lines); ClairS-TO Source Data workbook · Supplementary Table 7b, Dataset 'COLO829', Caller 'Pisces', Tumor coverage '50x', Type 'Indel', column 'TP'
Configuration: Pisces v5.3.0, tumour-only, Illumina (Chen et al. 2025)	Protocol: Illumina COLO829 tumour-only, 50x, somatic SNVs (Chen et al. 2025 Supplementary Table 7b) Dataset: COLO829 tumour Illumina NovaSeq 6000 WGS (ClairS-TO benchmark)	0.0635 AUPRC (SNV only, tumour-only, 50x tumour coverage) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Pisces on illumina-colo829 tumour-only SNV (Chen et al. 2025) somatic-clairs-to-20261011-protocol-illumina-colo829-snv Aggregation: Not reported ClairS-TO: a deep-learning method for long-read tumor-only somatic small variant calling; ClairS-TO Supplementary Information (Supplementary Tables 1-8 and command lines); ClairS-TO Source Data workbook · Supplementary Table 7b, Dataset 'COLO829', Caller 'Pisces', Tumor coverage '50x', Type 'SNV', column 'AUPRC'
Configuration: Pisces v5.3.0, tumour-only, Illumina (Chen et al. 2025)	Protocol: Illumina COLO829 tumour-only, 50x, somatic SNVs (Chen et al. 2025 Supplementary Table 7b) Dataset: COLO829 tumour Illumina NovaSeq 6000 WGS (ClairS-TO benchmark)	0.224 F1 (SNV only, tumour-only, 50x tumour coverage, at the best-F1 threshold) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Pisces on illumina-colo829 tumour-only SNV (Chen et al. 2025) somatic-clairs-to-20261011-protocol-illumina-colo829-snv Aggregation: Not reported ClairS-TO: a deep-learning method for long-read tumor-only somatic small variant calling; ClairS-TO Supplementary Information (Supplementary Tables 1-8 and command lines); ClairS-TO Source Data workbook · Supplementary Table 7b, Dataset 'COLO829', Caller 'Pisces', Tumor coverage '50x', Type 'SNV', column 'F1-score'
Configuration: Pisces v5.3.0, tumour-only, Illumina (Chen et al. 2025)	Protocol: Illumina COLO829 tumour-only, 50x, somatic SNVs (Chen et al. 2025 Supplementary Table 7b) Dataset: COLO829 tumour Illumina NovaSeq 6000 WGS (ClairS-TO benchmark)	6,085 False negatives (SNV only, tumour-only, 50x tumour coverage, at the best-F1 threshold) count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Pisces on illumina-colo829 tumour-only SNV (Chen et al. 2025) somatic-clairs-to-20261011-protocol-illumina-colo829-snv Aggregation: Not reported ClairS-TO: a deep-learning method for long-read tumor-only somatic small variant calling; ClairS-TO Supplementary Information (Supplementary Tables 1-8 and command lines); ClairS-TO Source Data workbook · Supplementary Table 7b, Dataset 'COLO829', Caller 'Pisces', Tumor coverage '50x', Type 'SNV', column 'FN'
Configuration: Pisces v5.3.0, tumour-only, Illumina (Chen et al. 2025)	Protocol: Illumina COLO829 tumour-only, 50x, somatic SNVs (Chen et al. 2025 Supplementary Table 7b) Dataset: COLO829 tumour Illumina NovaSeq 6000 WGS (ClairS-TO benchmark)	230,502 False positives (SNV only, tumour-only, 50x tumour coverage, at the best-F1 threshold) count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Pisces on illumina-colo829 tumour-only SNV (Chen et al. 2025) somatic-clairs-to-20261011-protocol-illumina-colo829-snv Aggregation: Not reported ClairS-TO: a deep-learning method for long-read tumor-only somatic small variant calling; ClairS-TO Supplementary Information (Supplementary Tables 1-8 and command lines); ClairS-TO Source Data workbook · Supplementary Table 7b, Dataset 'COLO829', Caller 'Pisces', Tumor coverage '50x', Type 'SNV', column 'FP'
Configuration: Pisces v5.3.0, tumour-only, Illumina (Chen et al. 2025)	Protocol: Illumina COLO829 tumour-only, 50x, somatic SNVs (Chen et al. 2025 Supplementary Table 7b) Dataset: COLO829 tumour Illumina NovaSeq 6000 WGS (ClairS-TO benchmark)	0.129 Precision (SNV only, tumour-only, 50x tumour coverage, at the best-F1 threshold) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Pisces on illumina-colo829 tumour-only SNV (Chen et al. 2025) somatic-clairs-to-20261011-protocol-illumina-colo829-snv Aggregation: Not reported ClairS-TO: a deep-learning method for long-read tumor-only somatic small variant calling; ClairS-TO Supplementary Information (Supplementary Tables 1-8 and command lines); ClairS-TO Source Data workbook · Supplementary Table 7b, Dataset 'COLO829', Caller 'Pisces', Tumor coverage '50x', Type 'SNV', column 'Precision'
Configuration: Pisces v5.3.0, tumour-only, Illumina (Chen et al. 2025)	Protocol: Illumina COLO829 tumour-only, 50x, somatic SNVs (Chen et al. 2025 Supplementary Table 7b) Dataset: COLO829 tumour Illumina NovaSeq 6000 WGS (ClairS-TO benchmark)	0.849 Recall (SNV only, tumour-only, 50x tumour coverage, at the best-F1 threshold) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Pisces on illumina-colo829 tumour-only SNV (Chen et al. 2025) somatic-clairs-to-20261011-protocol-illumina-colo829-snv Aggregation: Not reported ClairS-TO: a deep-learning method for long-read tumor-only somatic small variant calling; ClairS-TO Supplementary Information (Supplementary Tables 1-8 and command lines); ClairS-TO Source Data workbook · Supplementary Table 7b, Dataset 'COLO829', Caller 'Pisces', Tumor coverage '50x', Type 'SNV', column 'Recall'
Configuration: Pisces v5.3.0, tumour-only, Illumina (Chen et al. 2025)	Protocol: Illumina COLO829 tumour-only, 50x, somatic SNVs (Chen et al. 2025 Supplementary Table 7b) Dataset: COLO829 tumour Illumina NovaSeq 6000 WGS (ClairS-TO benchmark)	34,145 True positives (SNV only, tumour-only, 50x tumour coverage, at the best-F1 threshold) count · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Pisces on illumina-colo829 tumour-only SNV (Chen et al. 2025) somatic-clairs-to-20261011-protocol-illumina-colo829-snv Aggregation: Not reported ClairS-TO: a deep-learning method for long-read tumor-only somatic small variant calling; ClairS-TO Supplementary Information (Supplementary Tables 1-8 and command lines); ClairS-TO Source Data workbook · Supplementary Table 7b, Dataset 'COLO829', Caller 'Pisces', Tumor coverage '50x', Type 'SNV', column 'TP'

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

Use this configuration

How it works, versions and access

Strengths, limitations and unresolved questions

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.

0 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

No evidence rows match these filters. Choose another scope or clear the search.

How to read the evidence

Sources and history

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

3 source records and release history

ClairS-TO: a deep-learning method for long-read tumor-only somatic small variant calling · Original source · Nature Communications, published 2025-10-31; PMC12579226 full-text XML
ClairS-TO Supplementary Information (Supplementary Tables 1-8 and command lines) · Original source · Supplementary Information PDF (41467_2025_64547_MOESM1_ESM.pdf) of the published article
ClairS-TO Source Data workbook · Original source · Source Data file (41467_2025_64547_MOESM6_ESM.xlsx) of the published article

Download this release (gzip)

Technical metadata and extraction receipts

Stable ID: somatic-clairs-to-20261011-config-pisces-illumina

areas: dna-genomes
contexts: clinical_research
method types: conventional_pipeline
reported name: Pisces
version: v5.3.0
foundation model eligible: false
parameters: Tumour-only run with the authors' recommended settings (Supplementary Information command lines)
access reuse: Public software (Illumina)
source locator: Supplementary Information 'Command lines used'; Supplementary Tables 2 and 7 row labels
provenance note: Pisces as run on Illumina tumour-only data in the cited comparison.

Related records

configuration of: Pisces
system: Pisces on illumina-colo829 tumour-only Indel (Chen et al. 2025)
system: Pisces on illumina-colo829 tumour-only SNV (Chen et al. 2025)

Suggest a correction