Question: Questions about BreakDancer
0
gravatar for hxlei613
4.8 years ago by
hxlei61390
Bangladesh
hxlei61390 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 • 2.3k views
ADD COMMENTlink modified 4.8 years ago by trausch1.5k • written 4.8 years ago by hxlei61390
2
gravatar for trausch
4.8 years ago by
trausch1.5k
Germany
trausch1.5k 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 modified 10 months ago by RamRS30k • written 4.8 years ago by trausch1.5k
0
gravatar for Neilfws
4.8 years ago by
Neilfws49k
Sydney, Australia
Neilfws49k 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 modified 10 months ago by RamRS30k • written 4.8 years ago by Neilfws49k

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 4.8 years ago by hxlei61390
0
gravatar for michael.d.mclellan
4.8 years ago by
United States
michael.d.mclellan150 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.

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

ADD COMMENTlink modified 10 months ago by RamRS30k • written 4.8 years ago by michael.d.mclellan150
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