Question: Questions about BreakDancer
gravatar for hxlei613
3.6 years ago by
hxlei61380 wrote:

I find that Breakdancer is designed to detect SVs. But there are many people saying that it can be used to detect  CNV. I get my breakdancer output and there are only INS, INV, DEL, ITX, CTX five types.

I don't know how other people detect CNV using breakdancer.

Can someone help me ? Thank you very much!

cnv breakdancer ngs • 1.9k views
ADD COMMENTlink modified 3.5 years ago by trausch1.3k • written 3.6 years ago by hxlei61380
gravatar for trausch
3.5 years ago by
trausch1.3k wrote:

Breakdancer is a paired-end structural variant (SV) detection method and CNVs such as deletions and tandem duplications do give rise to abnormal paired-ends (if they are not embedded in repeats) and hence, paired-end methods such as Breakdancer, Delly or Lumpy are able to detect CNVs. Copy-number genotyping, however, seems to work best using read-depth and for germline CNVs I would also recommend GenomeSTRiP but it does require multiple samples to model the read-depth distributions.


ADD COMMENTlink written 3.5 years ago by trausch1.3k
gravatar for Neilfws
3.6 years ago by
Sydney, Australia
Neilfws48k wrote:

According to the documentation the cpp version - use the command:


computes copy number by either BAM file or by library, the Perl version does not.

ADD COMMENTlink written 3.6 years ago by Neilfws48k

My version is breakdancer-1.4.5.

You mean columns 12 is the estimated copy number. I find that there are many NA in column 12. Do you know why this happened ?

ADD REPLYlink written 3.6 years ago by hxlei61380
gravatar for michael.d.mclellan
3.5 years ago by
United States
michael.d.mclellan140 wrote:

It would be better to use a more descriptive subject and describe the type of data you are dealing with.

To start you might read this.

* Duan J, Zhang J-G, Deng H-W, Wang Y-P (2013) Comparative Studies of Copy Number Variation Detection Methods for Next-Generation Sequencing Technologies. PLoS ONE 8(3): e59128. doi:10.1371/journal.pone.0059128


There are a variety of solutions customized for different data types and data sets:


Germline Population-based: GenomeStriP


* Handsaker RE, Korn JM, Nemesh J, McCarroll SA Discovery and genotyping of genome structural polymorphism by sequencing on a population scale. Nature genetics 43, 269-276 (2011) PMID: 21317889

CopyCat: 3 different simlilar softwares for slightly different types of CNV detection:


Read + VAF

Read Depth:

Exome/Capture-based + Read Depth + Sample A vs B: Varscan2


ADD COMMENTlink written 3.5 years ago by michael.d.mclellan140
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