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what tools to visualize structural variants VCF files?

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

dna-seq structural-variants browser
• 6,132 views • link
updated by Ram Ram • written by Ming Tommy Tang Ming Tommy Tang

1 answer

Gene app from iobio is the best option I know.

• 0 views • link
updated by Ram Ram • written by Carlos Borroto Carlos Borroto

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

• 0 views • link
updated by Ram Ram • written by Ming Tommy Tang Ming Tommy Tang

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.

• 0 views • link
updated by Ram Ram • written by Carlos Borroto Carlos Borroto

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