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.

• 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:
• 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/