NGS interview questions

9 questions, each with a worked answer

1. 1 What are the main quality-control checkpoints in an NGS workflow? Fundamentals Concept
2. 2 How would you distinguish biological variants from sequencing or mapping artifacts? Intermediate Scenario
3. 3 How do depth and breadth of coverage affect variant-detection confidence? Intermediate Concept
4. 4 When can PCR duplication distort apparent allele counts? Intermediate Scenario
5. 5 How do you identify contamination or sample swaps in sequencing data? Advanced Concept
6. 6 How do reference genome choice and pipeline versions affect variant calls? Advanced Troubleshooting
7. 7 What evidence would lead you to suspect index hopping rather than a genuine rare variant? Intermediate Troubleshooting
8. 8 A sequencing run has excellent yield but poor mapping rates. How would you investigate? Intermediate Scenario
9. 9 Design a variant-calling validation strategy for a low-frequency mutation assay. Advanced Practical

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