IonTorrentRunAcceptanceChecker

URS & FS — User Requirements and Functional Specification

This document describes the controlled interface and behaviour of IonTorrentRunAcceptanceChecker for Ion Torrent Run Acceptance Checker.

Domain limits and critical parameters

• • AQ20 Bases: Number of bases with quality ≥Q20 — measure of useful sequencing output.
• • Uniformity: Coverage evenness across target regions — critical for amplicon-type panels.
• • On-Target Rate: Fraction of reads mapping to target regions — enrichment efficiency.
• • Ion Torrent has unique error profile: homopolymer indels constitute >60% of all errors.
• • Polyclonality >30% irreversibly degrades data quality and cannot be compensated by depth.
• • Chip overloading (ISP density > max) causes cascading degradation of all metrics.
• ⚠️ CRITICAL:
• • Polyclonal ≤30%: Exceedance = template dilution or ISP degradation.
• • AQ20 ≥ Min: Below threshold = insufficient data for reliable variant calling.
• • Uniformity ≥80%: For amplicon panels below 80% = primer or PCR issues.
• • Raw Accuracy ≥98.5%: Below = chemistry degradation or worn chip.
• Critical parameters:
• • Polyclonal Rate: ≤ 30%
• • AQ20 Bases: ≥ Panel-specific minimum
• • Uniformity: ≥ 80%
• • On-Target Rate: ≥ 70%
• • Raw Accuracy: ≥ 98.5%
• 4. Panel-Specific Thresholds: Customize limits per panel and chip type.

URS — User Requirements Specification

input.csv contract

RunID,ChipType,PanelName,ISP_Density_K_mm2,MinISP_Density,MaxISP_Density,Polyclonal_Percent,MaxPolyclonal_Percent,AQ20_Bases_Million,MinAQ20_Bases_Million,Mean_Read_Length_bp,MinMeanReadLength_bp,Uniformity_Percent,MinUniformity_Percent,Duplication_Rate_Percent,MaxDuplication_Rate_Percent,On_Target_Rate_Percent,MinOnTarget_Rate_Percent,Raw_Accuracy_Percent,MinRawAccuracy_Percent,Total_Reads_Million,MinTotal_Reads_Million,ControlSequence_Pass,Phasing_Score,MaxPhasing_Score
ION-2026-RUN-001,530,Oncomine Comprehensive Assay v3,680,200,1200,18.5,30.0,2800,500,185,100,92.5,80.0,15.2,40.0,88.0,70.0,99.4,98.5,12,5,true,0.8,1.5
ION-2026-RUN-002,520,AmpliSeq Cancer Hotspot v2,1350,200,1200,42.0,30.0,380,500,142,100,65.0,80.0,55.0,40.0,58.0,70.0,97.8,98.5,4,5,false,2.1,1.5
ION-2026-RUN-003,510,BRCA1/2 Panel,450,200,1200,28.0,30.0,620,500,165,100,82.0,80.0,35.0,40.0,75.0,70.0,99.1,98.5,6,5,true,1.2,1.5

Input validation rules

FS — Functional Specification

Example output.json

{
  "utilityId": "iontorrentrunacceptancechecker",
  "utilityFolder": "IonTorrentRunAcceptanceChecker",
  "package": "LiquidBiopsy",
  "overallStatus": "PASS|WARNING|FAIL",
  "sourceFile": "input.csv",
  "processedAtUtc": "2026-06-10T00:00:00Z",
  "checks": [
    {
      "parameter": "RunID",
      "value": "ION-2026-RUN-001",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-001"
    },
    {
      "parameter": "ChipType",
      "value": "530",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-002"
    },
    {
      "parameter": "PanelName",
      "value": "Oncomine Comprehensive Assay v3",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-003"
    },
    {
      "parameter": "ISP_Density_K_mm2",
      "value": "680",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-004"
    },
    {
      "parameter": "MinISP_Density",
      "value": "200",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-005"
    },
    {
      "parameter": "MaxISP_Density",
      "value": "1200",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-006"
    },
    {
      "parameter": "Polyclonal_Percent",
      "value": "18.5",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-007"
    },
    {
      "parameter": "MaxPolyclonal_Percent",
      "value": "30.0",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-008"
    },
    {
      "parameter": "AQ20_Bases_Million",
      "value": "2800",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-009"
    },
    {
      "parameter": "MinAQ20_Bases_Million",
      "value": "500",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-010"
    },
    {
      "parameter": "Mean_Read_Length_bp",
      "value": "185",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-011"
    },
    {
      "parameter": "MinMeanReadLength_bp",
      "value": "100",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-012"
    }
  ],
  "criticalFindings": [],
  "warnings": [],
  "audit": {
    "inputHash": "sha256:<calculated at runtime>",
    "rulesVersion": "<utility executable version>",
    "documentation": "IonTorrentRunAcceptanceChecker.documentation.html"
  }
}

Traceability matrix

IQ/OQ/PQ test scenarios

QA/QC and change control

• Do not rename columns without updating validator, documentation and test set.
• Retain input.csv, output.json, executable version and checksum.
• Before production use, perform IQ/OQ/PQ or equivalent CSV/CSA verification.
• Critical limits shall be verified against the approved specification, registration dossier and local SOPs.
• The utility provides structured QC decision support; final release decision remains with QA/QP and approved procedures.