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Old 05-14-2012, 06:21 AM   #1
lukas1848
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Location: Germany

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Default single bam for breakdancer

Hi,

I have a single bam file that includes all mapped reads of my sample and I want to use breakdancer to find SV in comparison with my reference genome.

If I run bam2cfg.pl with my bam file, I don't get any output. Is this because breakdancer requires at least two bam files, one for my sample and one for a control, i.e. a control sample (which would be my reference genome)?
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Old 06-15-2012, 06:48 AM   #2
Irsan_Kooi
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Hi there,

I just ran breakdancer on a single sample...

[myprompt]$ breakdancer_max -d breakdancer_HelaOM20_ HelaOM20.cfg > SV_breakdancer_HelaOM20.ctx

So something else is happening

Irsan
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