Affymetrix® Genotyping Console™ Software

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Copy number polymorphism (CNP) analysis is performed using the Canary algorithm. Canary was developed by the Broad Institute for making copy number state calls in genomic regions with copy number polymorphisms. CNP analysis using Canary is supported in GTC 3.0.1 for the SNP Array 6.0. See Appendix G in the GTC 3.0.1 User Manual for more information on CNP analysis and the Canary algorithm.