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!
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.
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.
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:
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version 2.3.6
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 ?