Allele format in bed file

[Desai Shailesh]

hello everyone 

I have attached two photos. One is reference panel data, which I am using to merge my generated data (HPF1) with world reference data for downstream analysis. 

As you can see, there is a difference in format. My data is in nucleotide format, whereas other data is in number, so I tried --allele12 to make an equal type of format, but I found it was not compatible. because the reference panel is genotype data (from the Illumina array), and what the numbers indicate, I don't know. Is there any way to convert this numerical allele back into nucleotide (character) format?

And how can I know the mean of those numerical alleles, like the corresponding nucleotide?

Thank you. 

[Christopher Chang]

You'll need to ask the provider of the reference panel to provide allele codes.