How to create reference allele file in plink? (~50 SNPs)

Question

[eyb]

How to create reference allele file? How it should look like? I need to convert plink ped/map files to VCF and reference allele file is part of the pipeline. http://www.researchgate.net/post/How_to_convert_plink_files_to_VCF_or_other_easily_parseable_format2

I have the same data in impute2 GEN format. So I think I will be able to pull out information on which allele is a reference from there. However I am not sure about reference allele file formatting.

Can anyone show me an example of the file?

Thanks