From a main analysis with one gene list
When a main analysis is launched and there is a gene list added afterwards, then the corresponding CNV analysis, deriving either from FASTQ or from a CNV VCF file, will automatically contain a sub-analysis with the Gene list's results for this CNV. The filtered CNV from gene list sub-analysis will appear as nested in the CNV analysis.
From a main analysis where the results are restricted to the gene list
There are cases where the main analysis results are restricted to a specific gene list. The primary reason why the full results are not shown when a user has run a gene list analysis, is to ensure that no incidental findings are shown. In a clinical setting, it 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 was not intended to be known for legal and/or ethical reasons.
A main analysis can be launched with a selected gene list where, by selecting the option “Show only gene list sub-analysis results” on the workflow creation step, the main analysis results will be hidden, which means that they will be restricted to the gene list to exclude any secondary findings. If this analysis is used to launch a CNV sub-analysis, then the corresponding CNV component's results will also be restricted to the gene list's results automatically.
The group supervisor can make the main analysis and the CNV deriving from that analysis results visible again by selecting from the analysis options “View whole sample” or hide the main analysis result by selecting “Hide”.
Please note that in the CNV Browser, the results will not be restricted to the gene list but will include results that go beyond the selected genes.
On our sample viewers such as CNV Browser, IGV, JBrowse the results are not limited to the gene list.
From a CNV analysis where the main analysis has more than one (multiple) gene lists
If a main analysis has more than one gene list, then the corresponding CNV component of this analysis will not contain any filtered results from these gene lists. However, if you want to launch a specific gene list to the CNV sub-analysis, you can do it by clicking on the Analysis actions, the option "Launch Gene-List analysis":
