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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?

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  • $\begingroup$ Can you please show the first few lines of the .bim file? That will help to establish whether or not there is rs information in there for Plink to use. $\endgroup$
    – gringer
    Jul 13 at 9:02
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Answer from @user438383, converted from comment:

It seems likely your input .bim file probably doesn't have RSIDs either - is that the case?

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