Question: Which Multiscale Genome Browser Is The Best At Visualizing Structural Variants?
4
gravatar for Martin
6.5 years ago by
Martin40
Martin40 wrote:

Or which techniques or standards do you consider best when visualizing SVs (insertion, deletion, inversion, translocation, duplication)? Thanks.

ADD COMMENTlink modified 14 months ago by suman.kapoor70 • written 6.5 years ago by Martin40
7
gravatar for Aaronquinlan
6.5 years ago by
Aaronquinlan10k
United States
Aaronquinlan10k wrote:

While I admittedly haven't tried all visualization tools, the two that I do use and would recommend are IGV and Savant. IGV has a nice "split screen" mode for viewing "ends" of two disjoint genomic loci as described by a SV call w.r.t. the reference genome. Savant takes an alternate approach in that they use arcs to draw connections between disjoint loci. The height of the arc indicates distance and the color indicates type (del, inv, dup, etc.).

Ira Hall and I cover some of these aspects, with a particular focus on complex variation in this review.

ADD COMMENTlink written 6.5 years ago by Aaronquinlan10k
1
gravatar for Ming Tang
2.8 years ago by
Ming Tang2.4k
Houston/MD Anderson Cancer Center
Ming Tang2.4k wrote:

4 years later. Is there any other tools that can better visualize structural variants (vcf files)? 

ADD COMMENTlink written 2.8 years ago by Ming Tang2.4k

Bump this post. Still looking for a command line tool that can simply take screenshots with paired end annotations (split reads, everts, too far....)

ADD REPLYlink written 2.4 years ago by Zev.Kronenberg11k
1

This is what I found so far... https://github.com/crazyhottommy/DNA-seq-analysis/blob/master/visualize_structural_variants.md Not satisfied yet.

ADD REPLYlink written 2.4 years ago by Ming Tang2.4k
0
gravatar for madk00k
4.0 years ago by
madk00k330
Heidelberg
madk00k330 wrote:

Here's a link to my post about visualizing fusion breakpoints from RNA-seq data, which is quite similar to visualization of translocations.

 

ADD COMMENTlink written 4.0 years ago by madk00k330

Nice post, I have added your blog to the Planet.

ADD REPLYlink written 3.9 years ago by Istvan Albert ♦♦ 77k

Tnx, hopefully it will be useful for ppl who work on this topic

ADD REPLYlink modified 3.9 years ago • written 3.9 years ago by madk00k330
0
gravatar for suman.kapoor7
14 months ago by
suman.kapoor70 wrote:

Try using Strand NGS the elastic genome browser is too good to visualize large SVs.

ADD COMMENTlink written 14 months ago by suman.kapoor70
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