I am designing an IDT capture panel consisting of 31 genes for sequencing some FFPE tumor samples. In addition to calling small variants I would also like to use CNVkit to call copy number aberrations for the genes in the panel. Since this is a small panel with only ~ 1300 probes it seems like it would beneficial to spike in IDT's CNV Backbone panel which would add ~ 9000 probes spaced about every .34Mb. But, since I am interested in low frequency variants in the 31 genes and the CNV backbone is considerably larger than the main panel, to spike the backbone in at an equi-molar ratio would significantly increase sequencing costs. Would it be feasible to spike the backbone in at say a 1:10 ratio, targeting about 100x average coverage? If so, does it make more sense to treat the backbone targets as part of the panel for CNVkit analysis, or let the program consider them off target reads?