Question: How to keep the same alleles order between bim file and vcf file?
gravatar for jiumeng66
2.5 years ago by
jiumeng6630 wrote:

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?

snp plink • 1.2k views
ADD COMMENTlink modified 2.4 years ago by h.mon30k • written 2.5 years ago by jiumeng6630

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?

ADD REPLYlink written 2.4 years ago by Kevin Blighe63k
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