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Some programs such as zCall produce output with the alleles labelled as A/B. The files created on the link below are to update the A/B notation to the TOP alleles, thereby allowing the use of the strand and position files (Strand Files) to generate a data set on the forward strand of genome build of choice.

These files are formatted for use in plink with the –update-alleles command.

http://www.well.ox.ac.uk/~wrayner/strand/ABtoTOPstrand.html