The filters are applied in the order they are listed in this article.
- Low-quality genotype is replaced with unknown (missing).
- Low read depth genotype is replaced with unknown (missing).
- Low allele frequency genotype is replaced with unknown (missing).
- Variants present in <X% cells are removed.
- Cells with genotype information for <X% of (filtered) variants are removed.
- Variants mutated in <X% of (filtered) cells are removed.