Which Multiscale Genome Browser Is The Best At Visualizing Structural Variants?

Question

[Martin]

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

Answer 1

[Aaronquinlan]

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.

Answer 2

[Ming Tommy Tang]

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

[Zev.Kronenberg]

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

[Ming Tommy Tang]

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

Answer 3

[madk00k]

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

[Istvan Albert]

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

[madk00k]

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

Answer 4

[suman.kapoor7]

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