Question: Varscan copynumber running problem
gravatar for jinxinhao1988
21 months ago by
jinxinhao198860 wrote:


I am trying to call CNV using Varscan. It needs two samples, normal and tumor. but I run into the error message as follows:

Normal Pileup: normal.mpileup Tumor Pileup: tumor.mpileup Min coverage: 10 Min avg qual: 15 P-value thresh: 0.01 Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: 5 at net.sf.varscan.Copynumber.<init>( at net.sf.varscan.VarScan.copynumber( at net.sf.varscan.VarScan.main(

And the process halted.

My command line : java -jar ../../../software/VarScan.v2.3.9.jar copynumber normal.mpileup tumor.mpileup 007_008_glio --min-coverage 10

pileup files were generated using samtools with the command line:

samtools mpileup -f snp_1p19q.fa normal_sorted.bam > normal.mpileup

So I have no idea what has caused the error, Thank you for your help.

cnv varscan • 667 views
ADD COMMENTlink modified 21 months ago by chen1.9k • written 21 months ago by jinxinhao198860

I am facing the same issue, Please update if you come across any solution. Thanks

ADD REPLYlink written 21 months ago by mittu1602170

Hi, I use another set of data to generate pileup file, and the result is fine. The difference between the two sets of data is that if the adaptor sequence had been clean removed. And the other set of data was aligned with bowtie not bwa. I don't know if this is the reason. One of my colleagues also mentioned the Java version. I use java 1.8, and he recommended that may I can try 1.7. I hope that you can fix the problem soon.

ADD REPLYlink written 21 months ago by jinxinhao198860
gravatar for chen
21 months ago by
chen1.9k wrote:

I suggest you to file an issue at VarScan's github page

ADD COMMENTlink written 21 months ago by chen1.9k
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