PLINK BED format: how interpret 0, 1, 2

Question

[CaffeSospeso]

Hello,

I'm working with RAD-seq data in Stacks. And I obtained my final dataset in .PED format. Then I converted the plink PED file (.ped and .map) into a .BED format file using the following command:

plink -file input.plink --set-missing-var-ids "@_#" --make-bed --out output.file --allow-extra-chr --mind 0.3 --geno 0

And I was wondering how I should interpret the coding of the alleles: 0, 1 , 2. Given that I did not specify any '--recode' command I'm not sure what would be the correct interpretation:

Is it correct to interpret as:

0 homozygous for the major allele 1 heterozygous 2 homozygous for minor alleles

Answer 1

[chrchang523]

0 values correspond to the allele in the 5th column of the .bim file, and 2 values correspond to the allele in the 6th column. The 6th column value actually defaults to major, not minor.