I would like to create phylogenetic trees for 50 patients with breast cancer based purely on SNP VAFs as I don't have copy number variations. Although I've been having several issues with patients having less than 10 mutations, there are many examples with ostensible VAF differences where sciClone keeps returning just one cluster. Here's an example https://www.sendspace.com/filegroup/Wn8S9o8HzjkcUaLzTpR%2BIQ
Do you have any ideas on what is the default/lowest minimum depth of the software ? I've also read in another paper (PhyloSub) that choosing another platform might increase potential number of clusters you get, so I am interested in anything that someone has to suggest that works on the above data.