Question: Using BreakDancer output file with BreakDown
gravatar for tg25
10 months ago by
tg250 wrote:

Hello Everyone,

I am using BreakDancer for structural variant calling. I found a BreakDancer Protocol that I used to run the program on my pooled samples. At the end of this paper, in the section called Suggestions for Further Analysis there is information about another program BreakDown. In using BreakDown, I want to obtain the allele fraction of the structural variants in my BreakDancer outputs.

I found the BreakDown paper and I have download the BreakDown software. According to the ReadMe, I should be able to run : perl <BreakDancer configuration file> <SV file > .

When I run this command, using my pooled configuration file and an SV file from running BreakDancer, I get a cfg.tmp file that is empty. And I get the following in my error file

  • Use of uninitialized value in subtraction
  • Use of uninitialized value within @fields in pattern match

Is there someone who has used BreakDown? If so, can you please share your experience. I have looked at past questions (on Biostars and SEQanswers), but it seems like most people use BreakDancer and no-one has used BreakDown.

In the BreakDown paper, BreakDown was compared to THetA , if there is someone how has used the BreakDancer output with THetA, can you please share your experience.

And if you have used another program to obtain the allele fractions of the structural variants from BreakDancer outputs. Can you please share this program.

Thank you for your help.

ADD COMMENTlink modified 10 months ago • written 10 months ago by tg250

Hello Everyone,

The BreakDown program ran and completed. The output was in my .out file. ūüôā

I am still learning how to use Bash along with a variety of other programs. Please, don't judge.

I hope that the information in the post above helps people who want to use both BreakDancer and BreakDown.

ADD REPLYlink written 10 months ago by tg250
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