Problem Generating Copy Number Variants Using Varscan2.
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7.6 years ago
Jordan ★ 1.2k

Hi,

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

[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.

cnv copynumber • 2.9k views
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That is not the exact command from the website. They use varScan where you use varscan_cnv_output.

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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.

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Entering edit mode
7.6 years ago
dankoboldt ▴ 140

Jordan,

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).