Question: Visualize VarScan2 Copy Number Aberrations in IGV
gravatar for plumgwodehouse
3.2 years ago by
plumgwodehouse0 wrote:


Is there a tool to visualize focal and large scale SCNAs detected using VarScan2? I have multiple samples and would like to see them as adjacent tracks in IGV. The site recommends loading the data using the copy number format, however the example given is for array data. I am not sure how that translates for the output from VarScan2.

Any suggestions?

Thanks! ~Plum

ADD COMMENTlink modified 3.2 years ago by genomax68k • written 3.2 years ago by plumgwodehouse0

Is there a specific reason that you want to do it in IGV, as opposed to just making some nice plots using one of the many packages for doing that sort of thing?

ADD REPLYlink written 3.2 years ago by Chris Miller21k

Hi Chris,

Two reasons why I am keen on IGV - have loaded other tracks for related analyses and secondly, collaborators who are remote log in and visualize our data in IGV.

Thanks, Plum

ADD REPLYlink written 3.2 years ago by plumgwodehouse0

Hi Plum, Did you ever figure out how to do this? I'm trying to do the same. Thanks!

ADD REPLYlink written 4 months ago by olechnwin0

The primary issue is that most copy number events are of size megabase or more. IGV works best on the base-to-kilobase scale. You certainly can make bed-like tracks that show your CN event, but it's probably not going to be the most helpful view..

ADD REPLYlink written 4 months ago by Chris Miller21k

I don't think size is the problem. IGV supports SEG file and in their example.seq some of the segment is >15Mbp SEG file format. I tried to modify the cbs file generated by varScan to match their example.seq file but it just doesn't display the same way...

ADD REPLYlink modified 4 months ago • written 4 months ago by olechnwin0
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