Help with allele flip in plink
1
0
Entering edit mode
11 days ago
MAPK2 ▴ 40

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
plink • 106 views
ADD COMMENT
0
Entering edit mode
10 days ago

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

ADD COMMENT

Login before adding your answer.

Traffic: 734 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6