Answers.Body: <p>Preferences <code>-&gt;</code> Alignments <code>-&gt;</code> Hide indels &lt; 'x' bases.</p>
  
  <hr>
  
  <p>Credit to <a href="https://www.biostars.org/p/339007/" rel="nofollow noreferrer">Pierre Lindenbaum</a></p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-01-02T22:10:34.813Z
Answers.LastActivityDate: 2020-01-02T22:10:34.813Z
Answers.UserDisplayName: Kohl Kinning
Body: <p>I am using IGV 2.5.2 and would not like to see the insertions  in my aligned reads. How can I do that? I have managed to remove mismatched bases because there is an option to do so when I right-click on the window ("Show mismatched bases"). Now I would like to do the same with these purple insertions.</p>
  
  <p><a href="https://i.sstatic.net/hxliq.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/hxliq.png" alt="IGV screenshot"></a></p>
  
  <h3>3rd January 2020 update</h3>
  
  <p><a href="https://i.sstatic.net/avy5K.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/avy5K.png" alt="IGV preferences"></a></p>
  
  <p>Thanks to a member's response, I found some parameter in the preferences that might be helpful to hide the indels. However, I have tried different numbers from 0 to 1000 and the indels are still shown. What numbers should I put to the parameters "Show indel threshold (bases)" and should I click the box or not?</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-01-03T19:33:50.280Z
Comments.Text: Check the box and try `1` as the threshold.
Comments.UserDisplayName: Kohl Kinning
Tags: <phylogenetics><visualization><igv>
Title: How can I not show insertions in the Integrative Genome Viewer (IGV)?
ThreadText: # How can I not show insertions in the Integrative Genome Viewer (IGV)?
  
  (Asked by: username_0 on 2020-01-01)
  
  I am using IGV 2.5.2 and would not like to see the insertions in my aligned reads. How can I do that? I have managed to remove mismatched bases because there is an option to do so when I right-click on the window ("Show mismatched bases"). Now I would like to do the same with these purple insertions.
  
  [![IGV screenshot](https://i.sstatic.net/hxliq.png)](https://i.sstatic.net/hxliq.png)
  
  ### 3rd January 2020 update
  
  [![IGV preferences](https://i.sstatic.net/avy5K.png)](https://i.sstatic.net/avy5K.png)
  
  Thanks to a member's response, I found some parameter in the preferences that might be helpful to hide the indels. However, I have tried different numbers from 0 to 1000 and the indels are still shown. What numbers should I put to the parameters "Show indel threshold (bases)" and should I click the box or not?
  
  **Tags:** phylogenetics, visualization, igv
  
  > **Comments:**
  > **username_1**: Check the box and try `1` as the threshold.  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2020-01-02. Score: 3
  
  Preferences `->` Alignments `->` Hide indels < 'x' bases.
  
  ---
  
  Credit to [Pierre Lindenbaum](https://www.biostars.org/p/339007/)
  
  
  ---
  
  