<p><em>Answer from @user438383, converted from comment:</em></p>
<p>It seems likely your input .bim file probably doesn't have RSIDs either - is that the case?</p>

CC BY-SA 4.0
2021-07-13T09:01:51.397Z
2021-07-13T09:01:51.397Z
gringer
<p>I'm using plink (1.9b5) to do allelic association. My problem is that my output does not write the <code>rsID</code> (SNP), it just writes a dot.</p>
<p>Output:</p>
<pre><code>CHR SNP  BP   A1  F_A      F_U      A2  P       OR           
1   .    1014 A   0.18     0.07     C   0.22    3.03
</code></pre>
<p>My script:</p>
<pre><code>plink --bed file.bed --bim file.bim --fam file.fam --make-bed --out output
</code></pre>
<p>Can someone please help me see what I'm doing wrong?</p>

CC BY-SA 4.0
2021-07-13T09:02:47.453Z
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.
gringer
<snp><phylogenetics><ngs><plink>
Output of allelic association doesn't write the rsID
# Output of allelic association doesn't write the rsID

(Asked by: username_0 on 2021-07-09)

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?

**Tags:** snp, phylogenetics, ngs, plink
> **Comments:**
> **username_1**: 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.  

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## 1 answers

### Answer by username_1 on 2021-07-13. Score: 0

*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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