I have done the imputation of my GWAS data with MACH. I would like to create a PED file with allele coding (AA, AT etc) not the dosage. Could you please suggest me how do it? Is there any software available to do this?
Given our experience and recent trends, the better choice for imputation is IMPUTE v2. Can you impute with this instead?
See GTOOL -G option: GEN to PED Conversion mode.
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