I 've WXS and WGS sequencing data and I would like to make somatic mutation calling and copy number calling. For the first one, I think I would use Strelka or MuTect2 but I've my doubts about how to obtain the copy number calls. Bearing in mind that, among other things, I would like to run clonality softwares such as PhyloWGS, EXPANDS and/or SciClone and therefore, I would need total copy number and/or allele-specific copy number calls for some of them, which are the best tools to do so?
In addition, for some of the samples I also have microarray data . Which is the best tool to obtain the copy number calls in this case?