Maximum total copy number

[SunDionel]

It seems to me that I need to set a limit for maximum total copy number in order to reduce computation time. The documentation says that if it is not specified, normal copy number is used. That makes me confused about what maximum copy number stands for. Is it the copy number for the matched normal? If it were the maximum copy number for the tumor sample, why would normal copy be the default limit?

Also, I am able to set the limit separately for each chromosome, which is great. However, for that, do I need to know the subclonal composition of my samples beforehand? I actually have multiple samples, so I was hoping to set maximum copy numbers per chromosome per sample.