Copy number variant from SNP array

Question

[enburns]

Does anyone know if there is a way to determine copy number variants from a SNP array? I have read that it is doable with some arrays but can't find how. Thank you for the help.

[John]

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)

Answer 1

[Eric T.]

Try the R package PSCBS.