Question: Why Does Breakdancer Work Without Reference Genome ?
1
gravatar for madkitty
6.5 years ago by
madkitty570
Canada
madkitty570 wrote:

I was wondering how Breakdancer is able to identify SV without telling him where is the reference genome ??

Also do you know if there's an option to compare 5 independant samples with breakdancer?

breakdancer cnv • 1.9k views
ADD COMMENTlink written 6.5 years ago by madkitty570

what do you mean by independant samples?

ADD REPLYlink written 6.5 years ago by Leszek3.9k

I mean samples that are not related to each other (not from the same group). For example if I want to compare SV from 5 different ethnicities and explore differences, SV arising in a certain group and not the others .. do we have such options with Breakdancer ?

ADD REPLYlink written 6.5 years ago by madkitty570
1

not sure. maybe you can run bd separately, and then parse/compare results between groups?

ADD REPLYlink written 6.5 years ago by Leszek3.9k
5
gravatar for Leszek
6.5 years ago by
Leszek3.9k
IIMCB, Poland
Leszek3.9k wrote:

That's wrong. Breakdancer takes alignment as input (BAM). Correspondence between your sample(s) and reference is present in that alignment.

ADD COMMENTlink written 6.5 years ago by Leszek3.9k
0
gravatar for mark.dunning
6.5 years ago by
mark.dunning200
The University of Sheffield
mark.dunning200 wrote:

You can run breakdancer on multiple samples by having a configuration file that gives information about each sample you want to analyse. The easiest way to create such a file is using the bam2cfg perl script

bam2cfg.pl SampleA.bam SampleB.bam SampleC.bam

You should see separate lines in the config files giving the stats for the three bam files

Then when you run breakdancer, each SV it detects will be annotated with how many reads from the different libraries have supporting evidence for the SV. You could then parse out SVs that are only supported by one sample.

ADD COMMENTlink written 6.5 years ago by mark.dunning200
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