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Systematic error monitoring

Alongside quality control checks for individual samples, batch monitoring is also in place to detect systematic errors should they arise. Plate-level and site-level quality control metrics are routinely evaluated for contamination, sex mismatch, and poor quality CNV calling issues, to ensure the genome is suitable for variant prioritisation.

  • Metrics for batch monitoring of contamination levels: Fraction of contaminated samples vs all delivered samples is determined per plate. This will allow for investigation of adjacent wells in a plate for potential below-threshold contamination.
  • Metrics for batch monitoring of samples with sex mismatches: Fraction of samples with conflicting inferred and reported sex vs all delivered samples is determined per plate. Using these metrics, issues such as unexpected plate rotation will be readily identifiable.