combine individuals and pool in the same multiplex?

[efinlay]

I want to perform targeted resequencing of genes for SNP discovery and CNV analysis.
I'm sequencing genes in cattle, mostly working within one breed but I'd also like to include other breed and some bovini outgroups. I'm considering the best multiplex design to maximise discovery on a limited budget.

By indexing individuals and multiplexing them before sequencing I can assign each sequence to an individual but will need to perform as many library preparations as I have individuals.

If I pooled individuals before carrying out a library prep I could reduce time and money on library preps but couldn't relate sequence back to an individual, I could only get allele frequencies but not genotypes.

Has anyone ever combined both strategies in a single library?
I'm imagining something like Barcodes 1 - 10 = Individuals 1-10
Barcode 11 = a pool of ten individuals from a different breed.

There would be issues about quantities of each to put in for the sequencing but has anyone tried or read about a similar strategy?

Thank you for your help