Ensuring each row is a connected read, in split screen mode

[Cath Tyner]

IGV Desktop v 2.8.0

Hello, 

I'm new to IGV. I've been searching the IGV Help pages and I have watched all the video tutorials, but I can't seem to find the answer - I may be missing something obvious due to being new at IGV! Please see the attached screenshot, which shows a single-panel view of 2 variants. I am trying to determine phase of the 2 variants. I can follow the thin line and thus prove to myself that they are in the same read, and thus these variants appear to be in cis; on the same chrom.

I now want to see these variants in a split panel, and so I have entered the two coords with a space in between them, and I can now see the variants in a split window. However, I am not sure if I'm looking at the equivalent view as the single panel, where I was able to follow the thin gray line from one variant to another to endure same reads. I have tried to right-click on the rows and then I selected "view as pairs", is that the only sorting that I need to do to ensure that the split screen is showing each row that is connected by the think gray line? Or do I also need to select "Group alignments by....(some other option)"?

Thank you for any assistance you can provide, and I apologize for the remedial question! 

[James Robinson]

Hi,  sorry this is not possible currently.  Each panel in a split screen view is independent, alignments will not show connections between them.   This is in our long term plan.

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[Cath Tyner]

Ah, ok. Thank you for the quick reply, James!

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