Why Does Breakdancer Work Without Reference Genome ?

Question

[madkitty]

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?

[Leszek]

what do you mean by independant samples?

[madkitty]

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 ?

[Leszek]

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

Answer 1

[Leszek]

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

Answer 2

[mark.dunning]

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.