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>(Copynumber.java:693) at net.sf.varscan.VarScan.copynumber(VarScan.java:328) at net.sf.varscan.VarScan.main(VarScan.java:209)
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.