effect allele #110
Description
Dear developers,
first of all congratulations and thanks a lot for the great tool!
I have a question about GWAS ouputs. I used rMVP to conduct gwas analyses using plink binary files as input (derived from a vcf containing biallelic SNPs). What I don't understand from the output is which one is the effect allele (i.e., the allele for which the effect size is estimated). Is it always the minor allele? Or the one that is coded as “1” in the input genotype data (in this case it should be the alternate, because I checked the .bim plink file and I think the alternate is reported as first allele).
Many thanks for your help