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Old 12-27-2013, 11:23 AM   #7
Location: Sao Paulo, Brazil

Join Date: Apr 2011
Posts: 17


i'm using separated mpileup (normal and tumoral) with -B option and VarScan 2.3.6 and getting the error :

Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException

The error goes away if i don't use a reference fasta file in mpileup command (-f).

I've rebuilt the index for fasta files and still getting the same error...

Any help or ideas would be great. i'm running mpilup again with no reference file just for copynumber pipeline for now...
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