Hi, I'm trying to detect somatic copy-number alterations in custom-targeted sequencing panel.
Most of the tools and methods published for this sake requires matched normal sample or panel of normals. However, we have no normal samples. We do have dozens of tumor samples sequenced with the same targets on with the same library prep methods, so, I believe we will be able to reduce the biases introduced by the target capturing and library preparation.
Did anyone tried to call somatic CNV with such "panel of tumors"? or familiar with tools that are less sensitive to this kind of setting? Best!