How to prepare input file for PolarMorphism?

[TinaNeik339]

Hi, I have a vcf file, how do I use it to convert to the format that PolarMorphism requires? What does 'a1' and 'a2' referring to?

This is my GWAS result output file format:

SNP Pos P.value MAF nobs H&B.P.Value Effect
C01:64A, G C01 64 0.182975714 0.253633721 688 0.586909086 -2.165878893
C01:109A, T C01 109 0.359687861 0.390988372 688 0.754468301 -1.909093707
C01:168A, G C01 168 0.294075359 0.093023256 688 0.702335864 2.224919696
C01:249A, G C01 249 1 0 688 1 NA
C01:261A, G C01 261 0.004262582 0.489825581 688 0.111812272 16.54683517
C01:263A, C C01 263 1 0 688 1 NA

How do I extract 'a1' and 'a2'?

Appreciate your feedback.

Thank you.

Tina