what tools to visualize structural variants VCF files?

Question

[Ming Tommy Tang]

I have structural variant calls in VCF format. what tools do you use for visualizing? I loaded into IGV, but I am not sure whether IGV is designed for SNVs, and the output is hard for me to interpret.

I have read these two posts:

1. Best Genome Browser To Look At Structural Variation Calls
2. Which Multiscale Genome Browser Is The Best At Visualizing Structural Variants?

Thanks,
Ming

Answer 1

[Carlos Borroto]

Gene app from iobio is the best option I know.

[Ming Tommy Tang]

This one is cool, but not optimal for structural variants.

[Carlos Borroto]

Somehow I missed the structural variant requirement. You are right, iobio is aimed at SNPs and small INDELs with functional annotations. I'm guessing for structural variants where functional annotations aren't as common or relevant, something else would be better.