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PyClone specifications


Unique identifier OMICS_03424
Name PyClone
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux
License GNU General Public License version 2.0
Computer skills Advanced
Version 0.12.7
Stability Stable
Maintained Yes


No version available


Publications for PyClone

PyClone citations


Outlier response to anti PD1 in uveal melanoma reveals germline MBD4 mutations in hypermutated tumors

Nat Commun
PMCID: 5951831
PMID: 29760383
DOI: 10.1038/s41467-018-04322-5

[…] Clonal evolution was inferred with Pyclone. Parameters used to define clusters of SNVs were: (i) at least five SNVs and (ii) mean cancer cell fraction of at least 10% in one sample. […]


Deterministic Evolutionary Trajectories Influence Primary Tumor Growth: TRACERx Renal

PMCID: 5938372
PMID: 29656894
DOI: 10.1016/j.cell.2018.03.043

[…] mous mutation. The driver events clusters were then ordered into a clonal hierarchy using TRONCO and presented as driver trees ().Clustering was performed on multi-region whole exome sequencing using PyClone Dirichlet process clustering (). For each mutation, the observed variant count was used and reference count was set such that the VAF was equal to half the pre-clustering CCF. Given that copy […]


Mixed ductal‐lobular carcinomas: evidence for progression from ductal to lobular morphology

PMCID: 5873281
PMID: 29344954
DOI: 10.1002/path.5040

[…] Supplementary materials and methods Supplementary figure legends Data S1. Pyclone analysis Figure S1. Detailed morphology and additional IHC of MDL1 Figure S2. Detailed morphology and additional IHC of MDL2 Figure S3. Detailed morphology and additional IHC of MDL3 Figure S4 […]


Whole exome sequencing reveals the origin and evolution of hepato cholangiocarcinoma

Nat Commun
PMCID: 5832792
PMID: 29497050
DOI: 10.1038/s41467-018-03276-y
call_split See protocol

[…] acquired on the corresponding branch and trunk. Driver mutational genes were marked on trunk and branch. In order to evaluate the clonality of tumor more precisely, we conducted clonal analysis using Pyclone. […]


Actionable perturbations of damage responses by TCL1/ATM and epigenetic lesions form the basis of T PLL

Nat Commun
PMCID: 5814445
PMID: 29449575
DOI: 10.1038/s41467-017-02688-6

[…] samples were compared in a pair-wise fashion: sample at F/U vs. sample at diagnosis. Estimations of cellular prevalences and clustering of mutated populations were obtained by the Bayesian framework PyClone using its own Binomial density model with 10,000 MCMC iterations and default priors (shape = 1.0; rate = 0.001; initial concentration = 1.0; alpha = 1; beta = 1). As input, we only considered […]


New therapeutic targets for pulmonary sarcomatoid carcinomas based on their genomic and phylogenetic profiles

PMCID: 5828205
PMID: 29535832
DOI: 10.18632/oncotarget.24365

[…] ations, and a phylogenetic tree was constructed []. The ‘ape’ and ‘phangon R’ (3.2.3 on linux) packages were utilized for these analyses.To estimate the fraction of cancer cells harboring a mutation, PyClone analysis was performed []. Mutations whose allele fractions were greater than 1% were regarded as significant and were utilized for in silico analyses. […]


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PyClone institution(s)
Bioinformatics Graduate Program, University of British Columbia, Vancouver, BC, Canada; Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, BC, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada; Department of Statistics, University of British Columbia, Vancouver, BC, Canada

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