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Old 10-29-2012, 08:27 AM   #1
Junior Member
Location: Germany

Join Date: May 2012
Posts: 2
Default Varscan exception error


I received the following error running Varscan.
I have run the program with the same command before without any problems:

Min coverage: 8x for Normal, 6x for Tumor
Min reads2: 2
Min strands2: 1
Min var freq: 0.2
Min freq for hom: 0.75
Normal purity: 1.0
Tumor purity: 0.6
Min avg qual: 10
P-value thresh: 0.99
Somatic p-value: 0.05
Exception in thread "main" java.lang.NumberFormatException: For input string: ":###AEHDAIJ#JE(DDG4EE#EDJEEEDJ>EIFGHFGJJJI)>JHIJHFIIGC#IDI=0GH?JG#G*FJFF#.IJFFICJGCIIEEIC#DJDD##DHDD#@DCCDC@"
at java.lang.NumberFormatException.forInputString(
at java.lang.Integer.parseInt(
at java.lang.Integer.parseInt(
at net.sf.varscan.Somatic.<init>(
at net.sf.varscan.VarScan.somatic(
at net.sf.varscan.VarScan.main(

any help?

moritzsch is offline   Reply With Quote
Old 11-08-2012, 07:42 AM   #2
Location: St. Louis

Join Date: Mar 2009
Posts: 62

This is a parsing error, usually encountered when VarScan is given an input file that's not the expected format. Can you provide your full command, as well as an excerpt from each of your input file(s)?
dkoboldt is offline   Reply With Quote
Old 11-08-2012, 08:09 AM   #3
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Location: Germany

Join Date: May 2012
Posts: 2

thanks, in the meantime I solved it
the pileup did not look properly and position and reference base were missing.

chr14..,..,,..,....,,,,..,,....,..,..,*,.,.C.,.,,,.,,.^X,^Z.^-. :###AEHDAIJ#JE(DDG4EE#EDJEEEDJ>EIFGHFGJJJI)>JHIJHFIIGC#IDI=0GH?JG#G*FJFF#.IJFFICJGCIIEEIC#DJDD##DHDD#@DCCDC@ Z>]>E]]E>2>>]]]>>>]]>>]]]]]]]]0]]]>]2]]]]]>>]]]]]]]>]]>]]>WWWWWWU>XUXXXX>VXX+XXXXXVXXXXXX>ZZZZ>>ZZZZWZZZZXZ-
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