IGV large deletions

Question

[Mohammad Amin]

This is my first time using IGV so I am a bit confused. Does the red track indicate the there is a a large deletion within that span?

Answer 1

[wakaruszka]

Hello. The red paired reads indicate that their insert size is unexpectedly large after mapping to the reference genome. This can be explained by a deletion in this region. In IGV, you should use the option: View as pairs; Color by insert size; Sort by insert size. This will help you visualize the deletion.