How to keep the same allele order of VCF and bim file?
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?
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This is not a "tool" type post, it is a Question. Read posts under https://www.biostars.org/t/how-to/, especially the main text of How to Use Biostars, Part II: Post types, Deleting, (Un)Subscribing, Linking and Bookmarking, where I mention: