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dkoboldt / varscan

Variant calling and somatic mutation/CNV detection for next-generation sequencing data
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varscan copynumber running problem #32

Open jinxinhao0627 opened 6 years ago

jinxinhao0627 commented 6 years ago

Hi, I am running Varscan copynumber using the default settings. But met this error message. 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.(Copynumber.java:693) at net.sf.varscan.VarScan.copynumber(VarScan.java:328) at net.sf.varscan.VarScan.main(VarScan.java:209)

My command line is: java -jar ../../../software/VarScan.v2.3.9.jar copynumber normal.mpileup tumor.mpileup 007_008_glio I have no idea what has caused the problem.

Thank you in advance.

sahirmohit commented 6 years ago

remove the positions with zero depth. awk '{if($4>0){print $0}}' normal.pileup >normal.nonzero.pileup awk '{if($4>0){print $0}}' tumor.pileup >tumor.nonzero.pileup java -jar VarScan.v2.3.9.jar copynumber normal.nonzero.pileup tumor.nonzero.pileup output_name