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CLONET: CLONality Estimate in Tumors


 CLONET Pipeline


CLONET is a collection of R scripts that allows:

  • computing global DNA admixture (1-purity) and ploidy of tumor DNA samples (each with matched normal sample) from sequencing data (WGS, WES, targeted)
  • computing clonality of each somatic aberration, including somatic copy number aberrations, point mutations, and structural rearrangements
  • nominatig the temporal relation among somatic aberrations and building evolution maps

CLONET scripts have the following common syntaxt:

CLONET.scriptName.R <ConfigurationFile.R>

Folders are organized as follows:

 -> Docs
 -> Examples
 -> Functions
 -> Tools

CLONET.R is the main R script required to compute global DNA admixture, ploidy and clonality of segmented data.
The Docs folder contains this document.
The Examples folder contains a folder Small that includes a complete run of all the CLONET scripts.
The Functions folder contains all the functions used by CLONET.
The Tools folder contains R scripts to perform point mutations (PM) analysis, structural rearrangement (RR) analysis and tumor evolution path analysis.


CLONET requires Linux kernel >= 2.6.15. CLONET requires R >= 2.7 and the following packages, parallel, dgof, sets, and pso, igraph, reshape2. CLONET requires global folder names. CLONET recommends ASEQ tool to generate initial pileup analysis (binaries provided).


Code by Davide Prandi
Laboratory of Computational Oncology (F. Demichelis)
Centre for Integrative Biology, University of Trento, Italy
email contacts:; demichelis@science.unitn.

CLONET is distributed under the MIT Licence.