I want to use a Read-Depth algorithm to call copy number alterations (CNAs) from Whole Exome Sequencing data (WES) of a specific tumor.
I have a set of WES tumor samples, some of which also have the matched normal sample. My question is: would be more effective, to call CNAs for each tumor, the whole set of matched normals or, if available, only the corresponding matched normal sample?
I thought that using only the single matched normal could spot only somatic variations, while using the whole set of normals would also add germline variations into account. Is that right?
Which best strategy do you suggest?