<p>Hi,</p>

<p>Is there a pipeline/pacakage that can easily get me genotypes (eg in AA, AG, GG) type format from Affy genome wide SNP CEL files. Thus far I've played around with Birdseed and CLRMM. Both suffer from a combination of being impossible to install, having awful documention or producing unusable output. I literally want, CEL files go in, (annotated!!!!) genotypes and confidence scores come out. Any suggestions?</p>

**Edit by Kevin Blighe on March 10, 2020**: Affymetrix was subsequently acquired by ThermoFisher, and the Genotyping Console can now be downloaded from <a href="https://www.thermofisher.com/br/en/home/life-science/microarray-analysis/microarray-analysis-instruments-software-services/microarray-analysis-software/genotyping-console-software.html">HERE</a>.

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<p><a href="http://www.affymetrix.com/browse/level_seven_software_products_only.jsp?productId=131535&amp;categoryId=35625#1_1">Affymetrix genotyping console</a></p>

<p>For SNP 6 it supports </p>

<ul>
<li>calling genotypes</li>
<li>copy number/LOH</li>
<li>copy segments data</li>
<li>copy number variation analysis</li>
</ul>

<p>Also <a href="http://media.affymetrix.com/support/downloads/manuals/gtc_4_0_user_manual.pdf">see manual</a></p>
