How do I distinguish between variants (e.g., SNVs) present in my cells (prior to editing) and actual edits?

If you are analyzing SNV edits, then it is a good idea to identify any SNVs in your wildtype cells that are not present in the reference genome you use. To do this, we recommend running a negative control for every experiment, where the base SNVs can be detected, separate from any editing that may occur. If these are present within your on- and off-target windows, you can modify the reference genome to match your sample, so that these SNVs will not be called in the GE pipeline.