Workflow Overview

CheckRef performs allele switch detection and correction through a series of automated steps.

Pipeline Summary

graph TD
    A[Input VCF Files] --> B[VALIDATE_VCF_FILES]
    B --> C[CHECK_ALLELE_SWITCH]
    D[Reference Legend Files] --> C
    C --> E{fixMethod?}
    E -->|remove| F[REMOVE_SWITCHED_SITES]
    E -->|correct| G[CORRECT_SWITCHED_SITES]
    F --> H[VERIFY_CORRECTIONS]
    G --> H
    H --> I[CREATE_SUMMARY]
    I --> J[Final Results]

Process Flow

1. Validation

• Check VCF file integrity
• Detect corrupted or empty files
• Verify VCF format compliance

2. Chromosome Matching

• Extract chromosome from filename
• Pair VCF with corresponding legend file
• Skip files without matches

3. Allele Switch Detection

• Extract common positions
• Compare REF/ALT orientations
• Identify mismatches
• Detect build incompatibilities

4. Correction/Removal

Remove mode: Exclude switched sites
Correct mode: Swap REF↔ALT alleles

5. Verification

• Re-check fixed VCF files
• Confirm all switches resolved
• Report any remaining issues

6. Summary Generation

• Aggregate statistics across chromosomes
• Calculate overlap percentages
• Generate final reports

See Also

• Process Flow - Detailed process descriptions
• Resource Usage - CPU/memory requirements
• Modules - Process reference