BACOM2: a Java tool for detecting normal cell contamination of copy number in heterogeneous tumor

Background BACOM is a statistically principled and unsupervised method to estimate genomic deletion type and normal tissue contamination, and accordingly recover the true copy number profile in cancer cells [1]. However, the average normal cell fraction estimated by BACOM was found higher than expected in TCGA ovarian cancer dataset. Results 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. Conclusion 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.