Dear Users,

I would like to know , that given I have only one tumor and its normal type and I have the sets of germline and somatic mutations with the frequency listed by VarScan2, how can I use this information along with the region information of this mutation corresponding to a gene , to outline the clonal and sub-clonal populations of mutation in the tumor. Is there any method that can help me generate a model which can help me understand which mutations are occupied in the entire tumor population and which less. This would help me understand all the sub clones of the tumor. In other way it will help me understand how the mutations are categorized in the entire tumor mass and also inform me to what extent this mutation is having a stake in the tumor. This classification helps to reconstruct the tumor fate and its evolution and will also enable me to list out the potential driver mutations and passenger mutations concerned with that tumor. Is there any tool that can help me do this? Most of the tools work on multiple samples. I would like to have some suggestions on these lines.
<p>We built the sciClone package for exactly this purpose: https://github.com/genome/sciclone</p>

<p>It takes inputs of somatic mutations, with readcounts and VAFs, and uses that information to infer subclonal populations in heterogeneous tumors. It also gives you some nice visualization options.</p>
