LiquidCgpRunQcChecker

URS & FS — User Requirements and Functional Specification

This document describes the controlled interface and behaviour of LiquidCgpRunQcChecker for Liquid CGP Run QC Checker.

Domain limits and critical parameters

• ENRICHMENT: On-target rate (≥60%), uniformity (≥80%), mean depth (≥10,000×), fold-80 penalty (≤2.0).
• UMI & ERROR SUPPRESSION: UMI dedup rate (≤85%), unique molecular depth (≥1,000×), duplication rate (≤40%).
• BACKGROUND & CONTROLS: Background noise (≤0.1% VAF), NTC pass rate (100%), positive control recovery (≥70%).
• DATA INTEGRITY: Index hopping (≤0.5%), UDI usage (mandatory).
• • Background >0.1% VAF makes reliable detection at VAF <0.5% impossible.
• ⚠️ CRITICAL THRESHOLDS:
• • Mean Depth ≥ 10,000× | Unique Molecular Depth ≥ 1,000×
• • Uniformity ≥ 80% | Background Noise ≤ 0.1% VAF
• • NTC Pass = 100% | Control Recovery ≥ 70%
• • Index Hopping ≤ 0.5% | UDI Mandatory

URS — User Requirements Specification

input.csv contract

RunID,PanelName,Platform,PercentQ30,MinQ30,ClusterDensity_K_mm2,MinClusterDensity,MaxClusterDensity,OnTargetRate_Percent,MinOnTargetRate,Uniformity_Percent,MinUniformity,MeanTargetDepth_X,MinMeanTargetDepth,Fold80_BasePenalty,MaxFold80,UMIDeduplication_Rate,MaxUMIDeduplication,UniqueMolecularDepth_X,MinUniqueMolecularDepth,DuplicationRate_Percent,MaxDuplicationRate,BackgroundNoise_VAF,MaxBackgroundNoise_VAF,NTCSamples_Total,NTCSamples_Pass,PositiveControl_Detected,PositiveControl_Recovery_Percent,MinPositiveControl_Recovery,IndexHoppingRate_Percent,MaxIndexHoppingRate,UDI_Used
LB-RUN-2026-001,OncoLiquid_500,NovaSeq 6000,89.2,75,920,800,1200,82.5,60,93.0,80,22000,10000,1.2,2.0,0.68,0.85,7200,1000,18.0,40,0.0002,0.001,4,4,true,95.0,70,0.05,0.5,true
LB-RUN-2026-002,OncoLiquid_500,NovaSeq 6000,71.0,75,1400,800,1200,48.0,60,65.0,80,6500,10000,3.5,2.0,0.92,0.85,520,1000,62.0,40,0.003,0.001,4,2,true,55.0,70,1.8,0.5,false

Input validation rules

FS — Functional Specification

Example output.json

{
  "utilityId": "liquidcgprunqcchecker",
  "utilityFolder": "LiquidCgpRunQcChecker",
  "package": "LiquidBiopsy",
  "overallStatus": "PASS|WARNING|FAIL",
  "sourceFile": "input.csv",
  "processedAtUtc": "2026-06-10T00:00:00Z",
  "checks": [
    {
      "parameter": "RunID",
      "value": "LB-RUN-2026-001",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-001"
    },
    {
      "parameter": "PanelName",
      "value": "OncoLiquid_500",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-002"
    },
    {
      "parameter": "Platform",
      "value": "NovaSeq 6000",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-003"
    },
    {
      "parameter": "PercentQ30",
      "value": "89.2",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-004"
    },
    {
      "parameter": "MinQ30",
      "value": "75",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-005"
    },
    {
      "parameter": "ClusterDensity_K_mm2",
      "value": "920",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-006"
    },
    {
      "parameter": "MinClusterDensity",
      "value": "800",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-007"
    },
    {
      "parameter": "MaxClusterDensity",
      "value": "1200",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-008"
    },
    {
      "parameter": "OnTargetRate_Percent",
      "value": "82.5",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-009"
    },
    {
      "parameter": "MinOnTargetRate",
      "value": "60",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-010"
    },
    {
      "parameter": "Uniformity_Percent",
      "value": "93.0",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-011"
    },
    {
      "parameter": "MinUniformity",
      "value": "80",
      "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": "LiquidCgpRunQcChecker.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.