CNV calling for non-WGS CNV analyses is also available in “Sensitive mode”. Compared to standard mode, a lower CNV detection threshold is applied, resulting in more sensitive calling and typically in a higher number of calls. CNV detection can be particularly challenging; for instance single exon CNVs can be hard to call. Still, in a clinical setting, the ability to detect such CNVs is of paramount importance. Sensitive mode is optimised for the needs of clinical laboratories. It allows a shift to the trade-off between recall and false discovery to benefit sensitivity, compared to the standard mode.
You can enable this feature for either somatic or germline samples (or both) in Preferences. Please, note that these settings are only available to the group administrator and any changes will be applied to all users of the group.