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?