Discarded Data

Table that summarizes the per-sample number of cells and variants that are discarded based on Advanced Filter settings. Low quality variants lists the number of variants that are removed from the data based on quality metrics like genotype quality score or read depth (typically 30 – 60% removed). Low quality cells lists the number of cells that are removed from the data based on quality metrics (typically below 5% removed). Low frequency variants lists the number of variants that are removed from the data based on fraction of cells for which a high-quality genotype is present (typically up to 90% removed).