From a quick search, it seems that Affymetrix Genotyping Console (GTC) is the only tool available for genotyping-- to be more specific, what I mean by genotyping is converting .CEL files to .CHP files with genotype calls.
The tool does not work on Mac, so I've been trying to install it on a Windows 10 desktop at work and it's been giving me all kinds of trouble. The problem I got stuck on is the SQL Server requirement. I installed and uninstalled SQL about three times now and still, GTC says it is not installed. I then checked their website and found out that Windows 10 is not officially supported...
So, is there an alternative out there? Preferably a command line tool that won't force me to deal with Windows?