How to create reference allele file in plink? (~50 SNPs)
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6.3 years ago
eyb ▴ 230

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

plink reference allele impute2 • 3.1k views
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