BACOM2 estimates tumor purity and average ploidy from Affymetrix SNP6 array data to help recovering the true copy number profile in cancer cells. It was developed on the base of original BACOM, and further added absolute normalization and precise quantification of somatic copy numbers.

BACOM2's MATLAB codes could be download here (download). It requires original BACOM program (download) to read and process raw SNP array data (.CEL files).

BACOM2's Java codes could be downloaded here (download). It could directly process .CEL files and gives tumor purity and ploidy estimation.

BACOM2's simulation data and program(MATLAB) could be downloaded here(download). For testing samples of real data, due to TCGA's policy we are required not to re-distribute the raw files that contain SNP information. Please visit TCGA website (link) to build your own data matrix: choose a disease of interest, and select Data Type as 'CNV(SNP array)', Data Level as 'Level 1', Center/Platform as 'BI(Genome-Wide-SNP-6)', Tumor/Normal as 'Tumor - matched' and 'Normal - matched', then apply the filtering. Access to protected data needs a data use certification (link).