[Breakdancer-help] BreakDancer run time

[Chao, K. (NIH/N. [F] <kat...@ni...>]

Hi,

I am new to using BreakDancer. I am trying to run breakdancer_max (version 1.4.5, perl) with three BAM files, and the documentation says, "This step normally takes 12 hours or so for three bam files, 8 hours or so for two bam files for cpp version, around three days for perl version." However, when I run breakdancer_max, the script only takes about 20-30 minutes, and it doesn't appear to throw any errors. The output .ctx file is not empty, but it does not contain the expected translocation.

Is there a reason why the script is running so much more quickly than expecting (and still producing output)?

Thanks.