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Old 10-01-2013, 06:55 AM   #5
sophiespo
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Location: australia

Join Date: Apr 2013
Posts: 15
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Hi Dan,

I was wondering if you could help me. I've been trying to get this particular aspect of VarScan2 working for a while.

I am creating my pileup then running VarScan like this:

Code:
samtools mpileup -B -q 1 -f reference.fa normal.bam tumour.bam > sample.mpileup

java -jar VarScan.v2.3.6.jar copynumber sample.mpileup output --mpileup 1
but I am still getting an error:

Code:
Min coverage:	10
Min avg qual:	15
P-value thresh:	0.01
Reading input from sample.mpileup
Reading mpileup input...
Parsing Exception on line:
chr1	3038588	c	0	*	*	0		
8
I am using a two-sample pileup and the -B flag like you've said, am I missing something?

Thanks
Sophie
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