Re: [Breakdancer-help] reference genome issue in breakdancer

[Ken C. <kc...@wa...>]

Yes.  I think the reference genome does not have to be the NCBI build or 
have finished quality. As long as the PE reads can be align to it, we 
should be able to identify SVs relative to the "reference".

-Ken

On 7/8/10 10:42 AM, Federica Torri wrote:
> 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...
>
>
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