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Viewing Rearrangements in BAM files

asked 2015-06-03 15:11:59 -0600

Brian Davis gravatar image

updated 2015-06-03 15:22:40 -0600

I very much like GenomeBrowse. However, I am examining complex rearrangements and structural variation in BAM files (detected by algoritms). I require the ability to easily identify which reads have a mate that maps to another chromosome, which reads have segments that do not map well partway through (and are therefore are perhaps retrogene or other insertion), which reads have larger or smaller insert sizes, etc... is this something that GenomeBrowse is able to do? It seems an obvious feature, and I can do so in IGV... but I far prefer GenomeBrowse if the functionality is available.

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answered 2015-06-05 11:18:25 -0600

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

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Hi! I just wanted to add my support for such features! The list you have would be awesome! I realize this was written in June...perhaps there's an update? The most significant for me would be your second bullet though the others would be pretty wonderful too. Thanks for a fabulous (& free) product!

Michele Wing ( 2015-11-23 16:21:37 -0600 )edit
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Asked: 2015-06-03 15:11:59 -0600

Seen: 61 times

Last updated: Jun 05 '15