Convert ATGC in PLINK to illumina AB

Question

[kiya89]

Hello.

I have PLINK data file (ATGC). But I want use illumina AB format.

How can I converting PLINK ATGC data format into illumina AB?

[Ram]

What have you tried?

[kiya89]

To change format, i tried using program like gengen etc. But, i couldn't get the result by error. Other try is that using PLINK --recode12 option. But, I don't know if the result is the same illumina AB.

[Kevin Blighe]

--recode12 is no the same. The Illumina AB format is quite specific, often called TOP / BOT format.

What commands have you tried with GenGen and what was the error(s)?