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  • Using Phylosub for Inferring clonality

    Hi,

    I have recently come across a paper which developed a software phylosub with which one can infer the clonal heterogenity in both single sample tumors or more samples. I have WES data of single sample tumor with its matched control. I would like to use the software but I do not see if anyone used or not? I am unable to understand how to prepare the data.txt input file which is used to detect the clonality. There is something as mu_v and mu_r column which is needed to be created. I am not sure how to do it. If anyone has experience I would like to know more about the way to create the data file. How to also get the values of delta_r and delta_v. It would be nice if any test sample is provided on which I can try with a test protocol. In my case I have bam files also I have vcf from VarScan2 which I have used to generate the columns for data.txt but I need to know how to do it for the rest columns like mu_r , mv_r, delta_r and delta_v. I would like some suggestions

    Regards

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