  We develop a cross-platform open-source Java application (BACOM2) with
graphic user interface (GUI), and users also can use a XML file to set the
parameters of algorithm model, file paths and the dataset of paired samples.
BACOM2 implements the new entire pipeline of copy number change analysis for
heterogeneous cancer tissues, including extraction of raw copy number signals
from CEL files of paired samples, attenuation correction, identification of
balanced AB-genotype loci, copy number detection and segmentation, global
baseline calculation and absolute normalization, differentiation of deletion
types, estimation of the normal tissue fraction and correction of normal tissue
contamination. BACOM2 focuses on the common tools for data preparation and
absolute normalization for copy number analysis of heterogeneous cancer
tissues. The software provides an additional choice for scientists who require
a user-friendly, high-speed processing, cross-platform computing environment
for large copy number data analysis.
