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hidden rowfor table layout
DescriptionClonal structure identification through penalizing pairwise differences
Development Information
GitHub wwylab/CliP
Languagepython (>3.5.1)
Current version0.1
LicenseArtistic (package)
Last updated2021/04/01
Citation Yujie Jiang, Kaixian Yu, Shuangxi Ji, Seung Jun Shin, Shaolong Cao, Matthew D Montierth, Licai Huang, Scott Kopetz, Pavlos Msaouel, Jennifer Rui Wang, Marek Kimmel, Hongtu Zhu, Wenyi Wang, and on behalf of the PCAWG Evolution and Heterogeneity Working Group and the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Network. CliP: subclonal architecture reconstruction of cancer cells in DNA sequencing data using a penalized likelihood model. (2021)
Help and Support
Contact Wenyi Wang 
Discussion Issues On GitHub 


CliP is a subclonal identification tool designed for next-generation sequecing of bulk tumor samples. It is one of the 11 participating methods in the Pan-Cancer Analysis of Whole Genome (PCAWG) working group, Heterogeneity and Evolution, of International Cancer Genome Consortium (ICGC). And the method is described in the manuscript (See Citation).


Need R(>3.3.1) and python(>3.5.1), the script does not support python2.


There is no need to install CliP.

Input data format:

CliP need 3 input files (please see Sample data for a more visualized example of input data):

SNV file: a tab separated file containing 8 columns. Specifically, it needs to include chromosome information, the position of the SNV, alt read, and ref read information. Please see the sample input for the detailed format.

CNV file: a tab separated file containing 6 columns. The first column denotes the chromosome, the second one is the start position of the CNV segment, the third column records the end position of the CNV segment. The last three columns takes the actual copy number of each segment, which are major & minor allele total and total copy number.

Purity file: A file containing the purity either an estimation from CNA or a guess that will be corrected hopefully by CliP. For details on purity issue, please check our manuscript.