LowVafSignalGateChecker

URS & FS — User Requirements and Functional Specification

This document describes the controlled interface and behaviour of LowVafSignalGateChecker for Low VAF Signal Gate Checker.

Domain limits and critical parameters

• Applies comprehensive gate to low-VAF variant calls: UMI family support (≥3 families, mean size ≥3), strand balance (ratio ≥0.3), binomial significance (p≤0.01), mapping/base quality, PoN/NTC exclusion, local background noise, and contextual checks (hotspot rescue, homopolymer/repeat warnings, gnomAD filter). Three-tier classification: ACCEPTED / REVIEW_REQUIRED / REJECTED. Compliant with CAP/CLIA, FDA liquid biopsy guidance, SEQC2.
• ⚠️ Critical: No reliable sub-1% calls without UMI. Strand bias is the most common FP indicator. PoN hit = artifact regardless of other metrics. Hotspot rescue downgrades to REVIEW_REQUIRED, not auto-accept.

URS — User Requirements Specification

input.csv contract

SampleID,VariantID,Gene,VariantType,ObservedVAF_Percent,TotalDepth,AltReads,ForwardAltReads,ReverseAltReads,UniqueMolecularFamilies,MinUMIFamilies,MeanFamilySize,MinMeanFamilySize,MappingQuality,MinMappingQuality,BaseQuality,MinBaseQuality,StrandBalanceRatio,MinStrandBalance,BinomialPValue,MaxBinomialPValue,FoundInPanelOfNormals,FoundInNTC,BackgroundNoiseAtPosition_VAF,MaxBackgroundNoise_VAF,IsKnownHotspot,IsInHomopolymerRegion,IsInRepeatRegion,GnomAD_AF,AssayLOD_Percent
LB-2026-001,EGFR:c.2573T>G,EGFR,SNV,0.35,18500,65,30,35,12,3,5.4,3.0,60,40,34,25,0.86,0.3,2.1E-15,0.01,false,false,0.0001,0.001,true,false,false,0,0.1
LB-2026-001,TP53:c.743G>A,TP53,SNV,0.22,15000,33,31,2,2,3,16.5,3.0,35,40,28,25,0.06,0.3,0.003,0.01,true,false,0.0018,0.001,false,false,false,0.0002,0.1
LB-2026-002,KRAS:c.35G>A,KRAS,SNV,0.18,22000,40,18,22,4,3,10.0,3.0,58,40,32,25,0.82,0.3,8.5E-10,0.01,false,false,0.0008,0.001,true,false,false,0,0.1

Input validation rules

FS — Functional Specification

Example output.json

{
  "utilityId": "lowvafsignalgatechecker",
  "utilityFolder": "LowVafSignalGateChecker",
  "package": "LiquidBiopsy",
  "overallStatus": "PASS|WARNING|FAIL",
  "sourceFile": "input.csv",
  "processedAtUtc": "2026-06-10T00:00:00Z",
  "checks": [
    {
      "parameter": "SampleID",
      "value": "LB-2026-001",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-001"
    },
    {
      "parameter": "VariantID",
      "value": "EGFR:c.2573T>G",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-002"
    },
    {
      "parameter": "Gene",
      "value": "EGFR",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-003"
    },
    {
      "parameter": "VariantType",
      "value": "SNV",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-004"
    },
    {
      "parameter": "ObservedVAF_Percent",
      "value": "0.35",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-005"
    },
    {
      "parameter": "TotalDepth",
      "value": "18500",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-006"
    },
    {
      "parameter": "AltReads",
      "value": "65",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-007"
    },
    {
      "parameter": "ForwardAltReads",
      "value": "30",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-008"
    },
    {
      "parameter": "ReverseAltReads",
      "value": "35",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-009"
    },
    {
      "parameter": "UniqueMolecularFamilies",
      "value": "12",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-010"
    },
    {
      "parameter": "MinUMIFamilies",
      "value": "3",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-011"
    },
    {
      "parameter": "MeanFamilySize",
      "value": "5.4",
      "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": "LowVafSignalGateChecker.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.