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I don't know about the tech these days, but 4 years ago we did it by genotyping the whole pedigree (Cytosnp), phasing the SNPs, and then looking for impossible allele combinations. I would always get 6 or 7 'impossibles' around CNVs.
If you have a CNV array then things are obviously a lot simpler - you simply look for regions of the genome which return non-0/50/100% signal intensity for the base called (using any of the many tools that plot that data)