Detecting rare CNVs with snp array data

Not sure if this is the right place to ask this, but does anyone have thoughts on the quality of current methods for detecting rare CNVs with SNP data? Are there problems to be aware of?

Its been a while since I’ve worked on rare CNVs, so not sure if there have been any advances in CNV methods, but it seemed PennCNV was the generally thought as the most robust method out there. I think PGC CNV group is still using the consensus calls from PennCNV + iPattern as their process. While we took any CNV > 20kb / 10 probes as our cutoff in the PGC SCZ study, I think > 100kb is what others have settled on for minimum size. One problem to be aware of is chips with exome/custom content that can lead to “chip-specific” CNVs and screw up meta-analysis

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Thank you, this is super helpful. We have psych array and now GSA+psych array–will have to see what chip-specific issues there might be.