How to keep the same alleles order between bim file and vcf file?

Question

[jiumeng66]

Hi, I am trying to convert bed/bim/fam files to vcf file using plink. However, I found that some alleles orders changed. For example, the allele order of rs1877179 in bim file is G/A, but changed to A/G in vcf file. But I need keep the same allele order between bim file and vcf file. I have tried add "--keep-allele-order", but this command did not work. So, what can I do?

[Kevin Blighe]

PLINK encodes variants as follows:

• Reference allele = major allele
• Variant allele = minor allele

Are you outputting just a subset of your data, perhaps, in which case the allele frequencies may have changed?