Affymetrix A/B allele coding to reference 'forward' allele coding manual conversion
I have a ped file with genotypes from the Genome-Wide Human SNP Array 6.0 array in their native A/B format. I need to convert these to the standard forward coding used by dbsnp and hg19. Does anyone have experience doing this?
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marcusanaymik •
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Sounds like a bit of a nightmare. Can you not obtain the original CEL files and re-call the genotypes? Take a look at Affy PowerTools, namely this: http://media.affymetrix.com/support/developer/powertools/changelog/apt-format-result.html