Question: Is there an allternative to Affymetrix GTC for Genotyping?
gravatar for novice
4.5 years ago by
United States
novice990 wrote:

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?


ADD COMMENTlink modified 12 months ago by freeseek100 • written 4.5 years ago by novice990
gravatar for freeseek
12 months ago by
freeseek100 wrote:

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.

ADD COMMENTlink written 12 months ago by freeseek100

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.

ADD REPLYlink written 12 months ago by GenoMax94k
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