20 months ago by
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 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/