See Li et al. 2008 for details. At “Analysis/Chromosome” with analysis method as “Copy number & LOH”, check “Options/Infer MCP” to infer major copy proportions (MCP). The inferred MCP values will be displayed as the inferred data at the genotype data view (use key “D” to toggle).

"Chromosome/Export SNP data" can export the MCP result. In the exported MCP data pair (such as "100, 0"), the first value divided by 100 is the inferred MCP (ranging between 0.5 and 1), and the second value is the inferred ordered genotype, taking the value 0, 1, 2, 3 for the genotype of minor and major copy alleles: SNP_A_A, SNP_B_B, SNP_A_B, SNP_B_A.

The current dchip will not use the normal contamination % in the sample information file; instead, the contamination will be reflected by inferred MCP greater than 0.5 but less than 1.