pyClone is a software used to infer clonal frequency estimates of a panel of deeply sequenced mutations. The software is a Bayesian hierachical model for inferring the frequency of cells with a given mutation from allelic count data generated by next generation sequencing experiments. PyClone makes use of prior information about genotype as well as jointly analysing all mutations in a sample.
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Sohrab P. Shah et al.
“The clonal and mutational evolution spectrum of primary triple-negative breast cancers”.
Nature 486, 395–399 (21 June 2012)