Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2021-07-13T09:01:51.397Z
Answers.LastActivityDate: 2021-07-13T09:01:51.397Z
Answers.UserDisplayName: gringer
Body: <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>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-07-13T09:02:47.453Z
Comments.Text: 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.
Comments.UserDisplayName: gringer
Tags: <snp><phylogenetics><ngs><plink>
Title: Output of allelic association doesn't write the rsID
ThreadText: # 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.  
  
  ---
  
  ## 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?
  
  
  ---
  
  