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Hey Brian,

I think your accurate in pointing out we don't have great support for investigating structural varinats currently. It's definitely something I'd like to improve.

A couple of things we are considering (feel free to comment/expanding on these):

• Option to show soft and hard-clipped sequences when hovering over reads, allowing to see sequences at breakpoints.
• Option to color reads by mate-pair distances, with a special color for mates on other chromosomes
• Option to color reads with strand inversions from their mates
• Option to have hover-labels configured to any of these useful properties (mates position, mate distances, etc)

Is there anything else IGV does to support this we should consider?

Thanks, Gabe