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.
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.