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CliP

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Overview
DescriptionClonal structure identification through penalizing pairwise differences
Development Information
GitHub wwylab/CliP
Languagepython (>3.5.1)
Current version0.1
LicenseArtistic (package)
StatusActive
Last updated2018/05/01
References
Citation Kaixian Yu, Seng Jung Shin, 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: fast subclonal architecture reconstruction from whole-genome sequencing data. (2018)
Help and Support
Contact Wenyi Wang 
Discussion Issues On GitHub 

CliP

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).

Prerequisitions

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

Installation

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 4 columns, the first column denotes the chromosome, the second one is the position of the SNV, the third column records alt read, and the last column denotes the ref read.

CNV file: a tab separated file containing 5 or 4 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. For the actual copy number of each segment, CliP accepts both total-only or allele specific 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.