Does anyone know any tools to detect copynumber variations (CNA) from matched tumor-normal sequencing data. There are tools like Battenberg and TitanCNA but they are intended to be used with WGS/WES data. My data, in turn, is a targeted sequencing data of 40 cancer genes. At least for Titan CNA my dataset is too small to be used.
Do you have any recommendations or tricks how to use my data for Batternberg/TitanCNA. From these option, TitanCNA would be more pleasing for me. As my project is related to tumor evolution, it is necessary to get information from CNA clonality.
Thank you in advance!