Question: Varscan, Using The Copycaller
gravatar for Mdeng
9.5 years ago by
Mdeng510 wrote:

Hi Folks,

After reading this question, I downloaded the VarScan program, but have some questions about how to use it.

I have 10 Samples, 2 from each patient, one tumor, one normal The data is from a Solid 4 sequencer, and is single end reads, 50BP in length.

So, it seems to be possible to get CNVs using the varscan copyCaller. But how to use it? "java -jar VarScan.v2.2.5.jar copyCaller -h" prints:

USAGE: VarScan copyCaller [output.copynumber] OPTIONS
    --regions-file    A list of regions (e.g. exons) to use for segmentation
    --output-file    Output file to contain the calls
    --min-coverage    Minimum read depth at a position to make a call [10]
    --min-region-size    Minimum size (in bases) for a region to be counted [10]

I am really not sure about the syntax and the input.

  • What is the input? Bam files? pileup files? Another format? If so, how does it look?
  • How do i use it? e.g. varscan copycaller normal.bam tumor.bam output.bam? (or same with pileup?)
  • Or is there any other "workflow", maybe pre and post analysis/steps?

With best,


varscan cnv • 6.0k views
ADD COMMENTlink modified 7.4 years ago by Biostar ♦♦ 20 • written 9.5 years ago by Mdeng510

Not a direct answer to your question, but I wrote this little python script: for performing this analysis starting from BAM files. There is a script to use R and the DNAcopy package to segment the results.

ADD REPLYlink written 9.5 years ago by Sean Davis26k
gravatar for Dan Koboldt
9.5 years ago by
Dan Koboldt60
Dan Koboldt60 wrote:


You should actually use the "VarScan copynumber" command, not "copyCaller", as the latter expects an old format. The input should be 1.) pileup or mpileup for normal sample 2.) pileup or mpileup for tumor sample

The command usage is like this: java -jar VarScan.jar copynumber [normal.pileup] [tumor.pileup] output-basename

The output of the above command will have the format: chromosome chr_start chr_stop normal_depth tumor_depth log2_ratio

You can feed this into a copy number segmentation program; I recommend the DNAcopy library of the BioConductor project.

Please e-mail me or post to the VarScan sourceforge forum if you have further questions.


Dan Koboldt dkoboldt [at] genome [dot] wustl [dot] edu

ADD COMMENTlink written 9.5 years ago by Dan Koboldt60


I am new at using varscan and did not know about the copynumber command. On your website its just listet in the java doc, isn't it?

Thanks a lot,


ADD REPLYlink written 9.5 years ago by Mdeng510


I am perfectly fine now. Everything worked. Now I am looking for a way to visualise this data. I think the R plots from the DNAcopy package don't look good with massive data. Is there maybe a way to load this data to IGV or use another plot?

With best,


ADD REPLYlink written 9.5 years ago by Mdeng510

Hi Mdeng,

Can you please share how did you end up visualizing your results from massive data.


ADD REPLYlink written 5.5 years ago by Chirag Nepal2.3k
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