Help with allele flip in plink

Question

[MAPK2]

Hi All,

I am trying to understand how allele flip works with plink. I thought it should generate strand flips, so I used the command below. However, my original.bim and flipped.bim alleles are still the same. Can someone please clarify what is wrong with my command? Thanks!

head flip_list
1:1052290
1:1127258

head original.bim
1       chr1:1052290:T:A        0       1052290 A       T
1       chr1:1127258:C:T        0       1127258 T       C


plink --bfile original --flip flip_list --make-bed --out flipped


head flipped.bim
1       chr1:1052290:T:A        0       1052290 A       T
1       chr1:1127258:C:T        0       1127258 T       C

Answer 1

[chrchang523]

The variant IDs in flip_list don’t match the ones in original.bim.