Question: Questions about BreakDancer
0
gravatar for hxlei613
23 months ago by
hxlei61380
Bangladesh
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 • 1.0k views
ADD COMMENTlink modified 23 months ago by trausch760 • written 23 months ago by hxlei61380
2
gravatar for trausch
23 months ago by
trausch760
Germany
trausch760 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 23 months ago by trausch760
0
gravatar for Neilfws
23 months ago by
Neilfws47k
Sydney, Australia
Neilfws47k wrote:

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

breakdancer_max

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

ADD COMMENTlink written 23 months ago by Neilfws47k

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 23 months ago by hxlei61380
0
gravatar for michael.d.mclellan
23 months ago by
United States
michael.d.mclellan120 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

* http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0059128

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

 

Germline Population-based: GenomeStriP

* http://www.broadinstitute.org/software/genomestrip/genome-strip

* 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:

Clonal: http://qb.cshl.edu/copycat/

Read + VAF https://github.com/abelhj/cc2/

Read Depth: https://github.com/chrisamiller/copycat

Exome/Capture-based + Read Depth + Sample A vs B: Varscan2 http://tvap.genome.wustl.edu/tools/varscan/

 

ADD COMMENTlink written 23 months ago by michael.d.mclellan120
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