which is the basis of our planned second release (PLINK 2.0).
See the homepage for updates taking it towards PLINO 2.0 alpha https://www.cog-genomics.org/plink/2.0/
We also have phased and annotated data for use in plink2.0 worked examples in GigaDB http://dx.doi.org/10.5524/100516
Analyzing Copy Number Variation using SNP Array Data: Protocols for
Calling CNV and Association Tests
Rare copy number variant (CNV) data