Question: Problem Generating Copy Number Variants Using Varscan2.
gravatar for Jordan
5.7 years ago by
Jordan1.1k wrote:


I'm trying to generate CNVs using Varscan2. But it does not seem to compile for me. I'm doing the exact command given from the website.

samtools mpileup -q 1 -f human_hg19.fa ~/Normal/BAM/normalfile.bam ~Tumor/BAM/tumorfile.bam | 
java -jar VarScan.v2.3.1.jar copynumber varscan_cnv_output --mpileup 1

It gives the following output and stops.

Min coverage:   10
Min avg qual:   15
P-value thresh: 0.01
File not found: varscan_cnv_output

[mpileup] 2 samples in 2 input files
<mpileup> Set max per-file depth to 4000

I'm not sure, what the problem is. Can anyone help? Thanks!

I got this command from the recommended workflow of the website. Here is the link.

copynumber cnv • 2.4k views
ADD COMMENTlink modified 5.6 years ago by dankoboldt140 • written 5.7 years ago by Jordan1.1k

That is not the exact command from the website. They use varScan where you use varscan_cnv_output.

ADD REPLYlink written 5.7 years ago by Neilfws48k

varscan_cnv_output is just the output file name, and so is varScan. I don't think the error is because of that. And I did try with varScan name too. I still get the same error.

ADD REPLYlink written 5.7 years ago by Jordan1.1k
gravatar for dankoboldt
5.6 years ago by
dankoboldt140 wrote:


Thank you for the message; I apologize for my delay in replying. Yes, this was a bug specific to mpileup files with the copynumber subcommand. I've just fixed it, and would be happy to send you an updated JAR file (just write me at dkoboldt (at) genome [dot] wustl [dot] edu).

ADD COMMENTlink modified 12 weeks ago by RamRS21k • written 5.6 years ago by dankoboldt140
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