For CNP discovery, we combined the genotype data from the Affymetrix and Illumina arrays and applied two algorithms, QuantiSNP27 and Birdseye5. First, approximately 60,000 CNP calls were made by each algorithm (~50 per sample), generally supported by data from both platforms. Shared genomic segments of common CNPs were identified and refined by an algorithm that used cross-sample correlations between nearby probes (Supplementary Information).
