I am trying BreakDancer for the first time in my lab and I thought I'd make a little post.
First off, these files have significant dependencies. Make sure you know how to work with cpan packages to get them installed before you embark into working with BreakDancer. I am working in Ubuntu so my notes on this process are likely to be less useful to most people, but just a heads up.
Secondly, you'll also want samtools installed, and preferably include its location in your path, if you plan to work with bam files. Anyone using BreakDancer with the bam file format (which I am, exclusively) will want to run bam2cfg.pl on their sample. I found that bam2cfg.pl has a hardcoded path to samtools, which is silly. You should edit lines 51 and 160 of this script to have your path to samtools.
Thirdly, all output is directed to std out. I don't think it mentions this in the readme. It'll save you a wasted run.
Also, it runs very quickly! I ran it on 14905688 PE Illumina reads and had results in less than 20 min on my Intel Core2 Quad CPU 2.66 GHz workstation.
I do want to mention that there is some bug (possibly my fault) where BreakDancerMini gives me the following error message:
repeatedly, though it still seems to work. Let me know, anyone, if you know what's up with that.
--Will
First off, these files have significant dependencies. Make sure you know how to work with cpan packages to get them installed before you embark into working with BreakDancer. I am working in Ubuntu so my notes on this process are likely to be less useful to most people, but just a heads up.
Secondly, you'll also want samtools installed, and preferably include its location in your path, if you plan to work with bam files. Anyone using BreakDancer with the bam file format (which I am, exclusively) will want to run bam2cfg.pl on their sample. I found that bam2cfg.pl has a hardcoded path to samtools, which is silly. You should edit lines 51 and 160 of this script to have your path to samtools.
Thirdly, all output is directed to std out. I don't think it mentions this in the readme. It'll save you a wasted run.
Also, it runs very quickly! I ran it on 14905688 PE Illumina reads and had results in less than 20 min on my Intel Core2 Quad CPU 2.66 GHz workstation.
I do want to mention that there is some bug (possibly my fault) where BreakDancerMini gives me the following error message:
Use of uninitialized value in subtraction (-) at BreakDancerMini.pl line 298, <$fh> line 433555
--Will
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