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Is there an allternative to Affymetrix GTC for Genotyping?

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?

Thanks.

genotyping microarray affymetrix
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updated by Giulio Genovese • Giulio Genovese • written by novice novice

1 answer

You can use the apt-probeset-genotype software as explained here with the additional option --cc-chp-output to generate single sample .CHP files with genotype calls. It works on Linux and it should work on Mac as well.

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written by Giulio Genovese • Giulio Genovese

Please create a tools post for your software package rather than posting it as an answer in multiple old threads. Here are examples of tools posts as a guide.

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written by GenoMax GenoMax

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