Calculation of allele frequency using 1000 genome project as reference panel

Question

[salvatore.dantona]

Good morning, I am looking for a way to calculate allele frequency for my dataset. I'd like to use the 1000 genome project files as reference panel. My file is structured in this way:

SNP effect_allele other_allele beta se pval Phenotype

rs10900604 A G -0.0198 0.0171 0.2471 xxx

rs11240777 A G 0.0195 0.0171 0.2520 xxx

rs11240779 A G -0.0181 0.0186 0.3292 xxx

rs11240780 T C -0.0189 0.0187 0.3113 xxx

Unfortunally I don't know which is the minor allele. I would use R, PLINK but I can't find a proper way with these tools (my file are not appropriate for PLINK and I can't find a proper R package for my purpose). Could you please help me? Thank you

[salvatore.dantona]

I didn't specify it, but I have the .bed .bim and .fam files of the 1000 genomes project, so the problem is specifically with my summary statistics

Answer 1

[salvatore.dantona]

Finally I found a solution. I used the list of SNPs in my summary statistics for the -extract command in PLINK. Thus, I selected only the SNPs of interest from European 1000genome project. After that, I used the -freq function, in order to calculate the minor allele frequencies (MAFs). The output file contains the list of the SNP, the minor alleles (A1s) and MAFs. With these new information, i checked if, for the same SNP, the A1s of the PLINK file were the same of the effect alleles in my summary statistics. If it was so, effect allele frequency = MAF. Otherwise, effect allele frequency = 1 - MAF. I hope that could be useful for other people having the same problem.