Process Flow

Detailed description of each process in the CheckRef pipeline.

Process Execution Order

1. VALIDATE_VCF_FILES - Parallel (one per VCF)
2. CHECK_ALLELE_SWITCH - Parallel (one per chromosome)
3. REMOVE_SWITCHED_SITES or CORRECT_SWITCHED_SITES - Parallel
4. VERIFY_CORRECTIONS - Parallel
5. CREATE_SUMMARY - Single process (aggregates all)

Parallelization

CheckRef automatically parallelizes across chromosomes:

• 22 autosomes + X, Y, MT can run simultaneously
• Each chromosome is independent
• No cross-chromosome dependencies
• Linear scaling with available resources

Error Handling

• Failed VCF validation → Skip chromosome
• Build mismatch detected → Graceful exit with message
• Process failure → Can resume with -resume
• Verification failure → Reported in logs

See Also

• Modules - Process details
• Resource Usage - CPU/memory needs