Question: How to keep the same allele order of VCF and bim file?
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gravatar for jiumeng66
2.5 years 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 tool alignment • 1.1k views
ADD COMMENTlink modified 2.5 years ago by RamRS28k • written 2.5 years ago by jiumeng6630

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:

If you have discovered or designed a new tool, share it with a Tool post. Remember, if you're looking for a tool, you have a Question, not a Tool

ADD REPLYlink written 2.5 years ago by RamRS28k
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