BayClone2: A Bayesian Sequence and Copy Number Caller for Subclones Using NGS Data
Juhee Lee, Peter Mueller, Subhajit Sengupta, Yuan Ji*
Introduction:For a heterogeneous sample with subclones, DNA nucleotide sequences and copy numbers can differ on multiple loci between subclones. To accurately estimate the number of subclonal variant allele, we must account for subclonal copy numbers. To our knowledge, there are no existing tools for jointly calling subclonal copy numbers and the corresponding variant allele fractions for the same loci. Most methods either call one of the two features while ignoring the other, or assume that one is known and call the other. The proposed method, BayClone2 (as an extension of BayClone (Sengupta et al., 2015)) provides a Bayesian solution using next-generation sequencing (NGS) data for joint inference on both, structure and sequencing variants within a subclone. In addition, BayClone2 estimates the number and cellular fractions of the subclones in the sample, thus providing a complete description of subclonal genetic structure. BayClone2 is implemented as an R package, and the source code is available at www.compgenome.org/bayclone2.
BayClone2 is currently licensed under the GPL version 3, BayClone2 may be distributed under GPL version 3.
Contact:Juhee Lee: email@example.com ; Subhajit Sengupta: firstname.lastname@example.org ; Yuan Ji: email@example.com
- Version 1.1 release - 12/25/2014
- We now have a R package at CRAN repository ( http://cran.r-project.org/web/packages/BayClone2/index.html ).
- Version 1.0 release - 09/22/2014
- BayClone2 is programmed using R and C++. R (http://www.r-project.org) needs to be installed to use BayClone2. For mac OSX, Xcode (IDE for Apple's OSX and iOS) needs to be installed.