Question: what tools to visualize structural variants VCF files?
6
gravatar for Ming Tang
3.8 years ago by
Ming Tang2.5k
Houston/MD Anderson Cancer Center
Ming Tang2.5k wrote:

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:

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

Thanks,

Ming

ADD COMMENTlink modified 3.8 years ago by Carlos Borroto1.9k • written 3.8 years ago by Ming Tang2.5k
2
gravatar for Carlos Borroto
3.8 years ago by
Carlos Borroto1.9k
Washington Metropolitan Area
Carlos Borroto1.9k wrote:

Gene app from iobio is the best option I know.

ADD COMMENTlink modified 15 months ago by RamRS25k • written 3.8 years ago by Carlos Borroto1.9k

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

ADD REPLYlink modified 15 months ago by RamRS25k • written 3.8 years ago by Ming Tang2.5k

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.

ADD REPLYlink modified 15 months ago by RamRS25k • written 3.8 years ago by Carlos Borroto1.9k
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