Currently, I am using cn.mops for detection of copy number variation in exome sequencing data. However, I encounter difficulty in choosing which function I should use. My project including tumor and corresponding control samples which point me to the referencecn.mops function while my sequencing data type(exome sequencing ) suggested that I should use exomecn.mops. I did not find any direction regarding this situation, so how should  I choose the algorithm?

referencecn.mops is the correct choice for your setting! The parameters of "exomecn.mops" are adjusted to a non-tumor copy number setting.