Why can't I use a gene list analysis for CNV calling?

In gene list analyses you can only access by default the results for the targeted genes and not the full parent analysis that is needed for the cohort of a CNV/SV analysis.
The primary reason we don't show the full results when a user has run a gene list analysis and we only show the results of the gene list, is to ensure we don't show incidental findings. In a clinical setting, is sometimes required that there be no way of seeing any information other than what the target regions include.  So, reporting a variant that falls outside the target genes might reveal something that wasn't intended to be known for legal and/or ethical reasons. This is why we don't allow such analyses to be included in CNV calling since that might find CNVs outside the genes' regions of interest and can cause issues.
If you know this is not a problem, you can choose to show the variants of the gene list's parent analysis:
Once you have done that, the analyses will be available for CNV calling. To avoid this, you can choose not to run a gene list analysis in the beginning and, instead, run a full analysis and then, once that is finished, run a gene list analysis separately. This will keep both analyses (full and gene list) visible to the user, making the full analysis available for CNV calling by default.