I run linear regression association test on PLINK, but as you all know, the output file only has A1 (minor allele). The basic output is: CHR Chromosome SNP SNP identifier BP Physical position (base-pair) A1 Tested allele (minor allele by default) TEST Code for the test (see below) NMISS Number of non-missing individuals included in analysis BETA/OR Regression coefficient (--linear) or odds ratio (--logistic) STAT Coefficient t-statistic P Asymptotic p-value for t-statistic
However, I want to use this association output file to run METAL analysis but it needs A2 (major allele) info. Therefore, does anyone know how to generate A2 data from my output assoc.linear test file?
Thank you all very much.