There are many programs out there to analyze tumour heterogeneity from multiregion sequencing (i.e. where multiple regions of a tumour are sequenced). Does anyone know a program that can do it for a single sample based on variant allele frequency (VAF)?
I can also create a custom code but I am unsure of whether my logic is sound, so any thoughts on the following? I have a list of neoantigens and their variant allele frequency. I would cluster them based on identical VAFs (i.e. neoantigens with the same VAF are binned together). Based on that clustering method, and creating a distance matrix, I would then create a dendrogram. One limitation of this is that it does not incorporate CNVs. Any other thoughts on my proposed method?
Thanks in advance for your help!