Which Multiscale Genome Browser Is The Best At Visualizing Structural Variants?
4
4
Entering edit mode
9.7 years ago
Martin ▴ 40

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

structural next-gen sequencing genome visualization • 5.5k views
ADD COMMENT
7
Entering edit mode
9.7 years ago

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 COMMENT
1
Entering edit mode
6.0 years ago
Ming Tang ★ 2.7k

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

ADD COMMENT
0
Entering edit mode

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 REPLY
1
Entering edit mode
ADD REPLY
0
Entering edit mode
7.2 years ago
madk00k ▴ 350

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

 

ADD COMMENT
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode
4.4 years ago

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

ADD COMMENT

Login before adding your answer.

Traffic: 1333 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6