(4) Remove variants genotyped in < X of cell
The Genotypes Called in Min % of Cells metric is the proportion of cells that have genotype information available. For example, a threshold of 80% retains only variants for which information is available in at least 80% of all cells. Variants with information in fewer than 80% of cells are removed
We recommend using a value of > 50%.
(5) Remove cell with < X of genotypes present
The Cells with Min % of Genotypes Called metric is the proportion of genotype information available on a per-cell basis. For example, a threshold of 80% retains only cells in which at least 80% of genotype information is available for any given variant.
We recommend using a value > 50 %.
(6) Remove variants mutated in < X of cells
The Variants Mutated in Min % of Cells metric is the percentage of cells across all cells with a genotype call that have a non-references genotype call (e.g., heterozygous or homozygous alternate).
The select threshold is dependent on the sample type and the scientific question one intends to address. For instance rare subclone detection require a lower threshold.