VariantCallAcceptanceChecker

URS & FS — User Requirements and Functional Specification

This document describes the controlled interface and behaviour of VariantCallAcceptanceChecker for Variant Call Acceptance Checker.

Domain limits and critical parameters

• • Depth Filtering: Context-dependent depth thresholds (≥20× germline, ≥100× somatic).
• • Strand bias (FS > 60) is the most frequent indicator of false-positive SNV.
• • Variant in negative control = systemic issue. All such calls must be rejected.
• ⚠️ CRITICAL:
• • Depth ≥ Context-Specific Min: Germline ≥20×, somatic ≥100× (for VAF <5%).
• • Strand Bias FS ≤ 60 (germline) / ≤ 200 (somatic): Exceedance = artifact.
• • QD ≥ 2.0: Low QD = variant not supported by base quality.
• • GQ ≥ 20: Below = uncertain genotype.
• Critical parameters:
• • Total Depth: ≥ Context-specific minimum
• • Mapping Quality: ≥ 40
• • Strand Bias (FS): ≤ Threshold
• • QualByDepth (QD): ≥ 2.0
• • Genotype Quality (GQ): ≥ 20
• 2. Panel of Normals (PoN): Use PoN from ≥40 samples to filter recurrent artifacts.
• 3. Orthogonal Validation: Confirm somatic calls with VAF <5% by ddPCR or amplicon-seq.

URS — User Requirements Specification

input.csv contract

SampleID,VariantID,VariantType,Context,TotalDepth,MinDepth_Germline,MinDepth_Somatic,AlleleBalance,MinAlleleBalance_Het,MaxAlleleBalance_Het,MappingQuality,MinMappingQuality,BaseQuality,MinBaseQuality,StrandBias_FS,MaxStrandBias_FS,ReadPositionBias_QD,MinQD,GenotypeQuality_GQ,MinGenotypeQuality,InControlSample,InGNomAD_PassFilter,CallerFilter,IsHomopolymerRegion,IsSegmentalDuplication
WES-2026-001,chr7:55249063:G:T,SNV,Germline,85,20,100,0.48,0.30,0.70,60,40,35,20,2.1,60,18.5,2.0,99,20,false,true,PASS,false,false
WES-2026-001,chr1:115256530:A:AT,Indel,Germline,45,20,100,0.35,0.30,0.70,38,40,22,20,125.0,60,1.2,2.0,15,20,false,false,LowQual,true,false
TUMOR-2026-001,chr12:25398284:C:A,SNV,Somatic,65,20,100,0.08,0.02,0.40,55,40,30,20,8.5,200,12.0,2.0,45,20,false,true,PASS,false,false

Input validation rules

FS — Functional Specification

Example output.json

{
  "utilityId": "variantcallacceptancechecker",
  "utilityFolder": "VariantCallAcceptanceChecker",
  "package": "LiquidBiopsy",
  "overallStatus": "PASS|WARNING|FAIL",
  "sourceFile": "input.csv",
  "processedAtUtc": "2026-06-10T00:00:00Z",
  "checks": [
    {
      "parameter": "SampleID",
      "value": "WES-2026-001",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-001"
    },
    {
      "parameter": "VariantID",
      "value": "chr7:55249063:G:T",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-002"
    },
    {
      "parameter": "VariantType",
      "value": "SNV",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-003"
    },
    {
      "parameter": "Context",
      "value": "Germline",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-004"
    },
    {
      "parameter": "TotalDepth",
      "value": "85",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-005"
    },
    {
      "parameter": "MinDepth_Germline",
      "value": "20",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-006"
    },
    {
      "parameter": "MinDepth_Somatic",
      "value": "100",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-007"
    },
    {
      "parameter": "AlleleBalance",
      "value": "0.48",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-008"
    },
    {
      "parameter": "MinAlleleBalance_Het",
      "value": "0.30",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-009"
    },
    {
      "parameter": "MaxAlleleBalance_Het",
      "value": "0.70",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-010"
    },
    {
      "parameter": "MappingQuality",
      "value": "60",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-011"
    },
    {
      "parameter": "MinMappingQuality",
      "value": "40",
      "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": "VariantCallAcceptanceChecker.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.