Affymetrix A/B allele coding to reference 'forward' allele coding manual conversion

Question

[marcusanaymik]

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?

[Kevin Blighe]

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