Which order are the advanced filters applied?

  • Updated

The filters are applied in the order they are listed in this article.

  1. Low-quality genotype is replaced with unknown (missing).
  2. Low read depth genotype is replaced with unknown (missing).
  3. Low allele frequency genotype is replaced with unknown (missing).
  4. Variants present in <X% cells are removed.
  5. Cells with genotype information for <X% of (filtered) variants are removed.
  6. Variants mutated in <X% of (filtered) cells are removed.
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