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  1. Gencove
  2. Deliverables and QC Metrics
  3. Quality Control Metrics

Quality Control Metrics

At the start of every Gencove project, you’ll be required to select the Project Configuration (PC) you’ll want to use (a.k.a pipeline). Our pipelines include a number of automatic quality control (QC) checks to ensure data integrity and quality. Examples of QC checks regularly performed are (1) a check for proper input data formatting; (2) number of bases sequenced; (3) number of bases aligned to the reference genome, and more. If a sample fails any QC check, the sample itself will be marked as failed and no results will be returned besides the input `FASTQ` files. Depending on the PC being used, there may or may not be additional QC checks performed. The general QC checks/metrics are as follows:

  • Bases sequenced
  • Aligned and duplicated reads
  • Maximum contamination by DNA from another sample of the same species
  • Number of variants in reference panel that are covered by at least one sequencing read / Minimum effective coverage
  • Heterozygosity/Homozygosity
  • Minimum call confidence

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