Split plink files from multiallelic to biallelic

Question

[MAPK]

I have plink (bed, bim, and fam) files with multiallelic variants. I was wondering if there is a way to split the multiallelic to biallelic in plink without going back to vcf and splitting them?

[chrchang523]

The premise of your question is wrong: bed + bim + fam CANNOT store regular multiallelic variants. The plink2 (pgen + pvar + psam) format can.

Please revise your question, and provide a few lines of example data to clarify what you are talking about.

[MAPK]

@chrchang523 My question is specifically about .bim file. For example, the third row is multiallelic. I just want them to split in two rows? Can I only split .bim file and keep other files as is without causing any trouble ?

1       chr1:930939:G:A 0       930939  G       A
1       chr1:930947:G:A 0       930947  A       G
1       chr1:930952:G:A;chr1:930952:G:C 0       930952  A       G

and get something like this:

1       chr1:930939:G:A 0       930939  G       A
1       chr1:930947:G:A 0       930947  A       G
1       chr1:930952:G:A 0       930952  A       G
1       chr1:930952:G:C 0       930952  A       G

[chrchang523]

You lost all but the two most common alleles when you imported the multiallelic variant from a VCF into plink 1.9. You need to backtrack to your VCF and redo everything from there, and you probably want to use plink 2.0 and —pfile/—make-pgen instead of plink 1.9 —bfile/—make-bed.

[sayyarsehrish]

hy chrchang i have to make pgen and psam file and after that --pca and got plink.eigenvec but it's now creating a problem in the R package for PCA grapgh