I plan to use a whole genome CNV backbone (~1Mbp target density) with a number of custom hybrid capture panels (~40 - 400 genes), but I have some concern about the following text from the CNVKit v0.9.8 Documentation:
If some targets are enriched separately for each sample via spike-in, rather than as part of the original capture panel (which is assumed to have a fairly consistent capture efficiency across targets for all test and control samples), then the spike-in capture efficiency will typically vary too much to be useful as a copy number signal. In that case, the spike-in region should not be included in the target BED file, and excluded from the access regions (which determine antitarget regions) by using the -x option
Does this refer to the case where the spike-in is prepared as a separate library and then combined with the main panel?
In my case the backbone probes will be spiked in with the custom panel probes prior to enrichment at a 1:5 or 1:10 ratio, so the enrichment will include all probes.
