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

3rd January 2020 update

IGV preferences

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?

  • $\begingroup$ Check the box and try 1 as the threshold. $\endgroup$ Jan 3, 2020 at 19:33

1 Answer 1


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

Credit to Pierre Lindenbaum


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