I'm using plink (1.9b5) to do allelic association. My problem is that my output does not write the rsID
(SNP), it just writes a dot.
Output:
CHR SNP BP A1 F_A F_U A2 P OR
1 . 1014 A 0.18 0.07 C 0.22 3.03
My script:
plink --bed file.bed --bim file.bim --fam file.fam --make-bed --out output
Can someone please help me see what I'm doing wrong?
.bim
file? That will help to establish whether or not there is rs information in there for Plink to use. $\endgroup$