How to run the tool on multiple samples from the same patient

[MigleMi]

Thank you for developing this tool, I am very excited to try it out on my data. However, I have a few questions about the way I should proceed and I hope you can help me out. I have several patients with multiple biopsies from the same tumor, which makes this tool ideal. The first problem I have is that most samples have very few normal cells, like ~50, so very high tumor content. There is one sample that is mainly stromal and immune cells, could I use this sample for other samples from the same patient, is there any problem with different batches or sequencing depth? Secondly, since I ran Numbat, I can see that there are different subclones in each sample, but my samples are all ~10k cells, I would like to subset my data based on Numbat clones and run SComatic. What would be a reasonable cell number to downsample each subclone? Also, how can I combine the whole analysis of all samples from each patient? should I split each sample bam file to smaller bams based on Numbat analysis and then run step 3 with all subclones from the same patient?