single bam for breakdancer

[lukas1848]

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)?

[Irsan_Kooi]

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