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broadinstitute / PhylogicNDT

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Min number of mutations in each cluster #39

Open mksamur opened 4 years ago

mksamur commented 4 years ago

what is the best approach to control cluster size? I run PhylogicNDT with WGS data and some clusters I found has less than 20 mutations. Usually these clusters have very low probability density with wide CCF variance as expected I think. Is there a way to control min cluster size directly or make PhylogicNDT ignore these clusters during the contraction of the tree and assign them to the most probable nodes later on?

mkinnaman commented 4 years ago

I am also running into a similar issue, would be great to be able to filter out clusters with less than 10 mutations during tree formation. I tried changing the pi_k_mu and pi_k_r values without much success.