[Breakdancer-help] reference genome issue in breakdancer

[Federica T. <fed...@un...>]

Hi,

I am starting to use brakdancer for CNVs detection on my NGS data. I am not dealing with tumor-normale studies, but I have sequences of individuals affected by a complex disorder. So, is it possible to run Breakdancer only on my sequences without a reference? 

I  mean, if the algorithm works calling abnormal pairs of reads in term of expected distance and orientation, seems to me possible that the presence of a reference genome would not be mandatory...if it is necessary to also have the bam of a control genome, you are using  some particular  "consensus" bamfile avalilable or a "sinthetic" reference genome?

Thanks a lot



Federica



Dr. Federica Torri, PhD

University of Milan 

Genomics and Bioinformatics Unit  

c/o Filarete Foundation, 

Viale Ortles, 22/4

20139 - Milano (IT)

e-mail: fed...@un...