IGV color codes for mate-pair data

[Samarth Kulshrestha]

Hi,

I am using IGV 2.1.30 for Structural rearrangements for our mate-pair data.

I am interested in visualization of Inversion events. I launch and upload my BAM files (mate-pair) to IGV interface for a specific Inversion location. When i change "color alignment according to pair orientation" I see lots of green colored reads (attachment) in both Case/Control data which is a case of Tandem Duplication (as mentioned in IGV tutorial).

Can you just explain why those Green colored reads are appearing in case of an Inversion event.

Thanks
Samarth Kulshrestha

[Jim Robinson]

Its simply coloring reads based on their left orientation  (left/right and strand).  IGV itself has no knowledge of specific events, of course, only of pair orientation.   Certain orientations can be evidence of, but not proof of, classes of events.  

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