Question: How to keep the same alleles order between bim file and vcf file?
0
gravatar for jiumeng66
7 months ago by
jiumeng6630
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 • 323 views
ADD COMMENTlink modified 6 months ago by h.mon19k • written 7 months 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 6 months ago by Kevin Blighe28k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1520 users visited in the last hour