Hi everybody As known, breakdancer uses the pair end way to call cnv. Its readme file says that with the CPP version, it's possible to call the copy number variants. However, I only found INS, INV, DEL, ITX, CTX five aberration types in the results. Anybody could tell me where I could find the cnv results information. Thanks in advance.
Breakdancer doesn't call copy number variants. It calls structural variants. If you see a large deletion in breakdancer, it may be the case that a copy number deletion has occurred. It's also possible that the deleted sequence got re-integrated somewhere else, in which case, there would be no effect on copy number.