PyClone parameters on simulated data

[edyta.k...@ardigen.com]

Hello,

I would like to recreate the results of PyClone run on simulated data, although for now I obtain higher number of clusters in comparison to reference even in samples with 100 mutations and the mutations are assigned differently to clusters. Is it possible to get optimal parameters used for simulated data described in publication while running PyClone?

Thanks,

EK

[Andrew]

If the results are drastically different, then I would suggest running PyClone longer. My notes suggest I was using 100,000 iterations and discarding the first 50,000 for the synthetic runs.