<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>

CC BY-SA 4.0
2020-01-02T22:10:34.813Z
2020-01-02T22:10:34.813Z
Kohl Kinning
<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>

CC BY-SA 4.0
2020-01-03T19:33:50.280Z
Check the box and try `1` as the threshold.
Kohl Kinning
<phylogenetics><visualization><igv>
How can I not show insertions in the Integrative Genome Viewer (IGV)?
# 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.  

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## 1 answers

### Answer by username_1 on 2020-01-02. Score: 3

Preferences `->` Alignments `->` Hide indels < 'x' bases.

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Credit to [Pierre Lindenbaum](https://www.biostars.org/p/339007/)


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