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Perreault et al. BMC Bioinformatics 2010, 11:226 /1471-2105/11/226 S O F T W A R E Open Access Software Partitioning of copy-number genotypes in pedigrees 1,2 2,3 1 1,2 Louis-Philippe Lemieux Perreault* , Gregor U Andelfinger , Géraldine Asselin and Marie-Pierre Dubé* Abstract Background: Copy number variations (CNVs) and polymorphisms (CNPs) have only recently gained the genetic communitys attention. Conservative estimates have shown that CNVs and CNPs might affect more than 10% of the genome and that they may be at least as important as single nucleotide polymorphisms in assessing human variability. Widely used tools for CNP analysis have been implemented in Birdsuite and PLINK for the purpose of conducting genetic association studies based on the unpartitioned total number of CNP copies provided by the intensities from Affymetrixs Genome-Wide Human SNP Array. Here, we are interested in partitioning copy number variations and polymorphisms in extended pedigrees for the purpose of linkage analysis on familial data. Results: We have developed CNGen, a new software for the partitioning of copy number poly morphism using the integrated genotypes from Birdsuite with the Affymetrix platform. The algorithm applied to familial trios or extended pedigrees can produce partitioned copy number genotypes with distinct parental alleles. We have validated the algorithm using simulations on a complex pedigree structure using frequencies calculated from a real dataset of 300 genotyped samples from 42 pedigrees segregating a congenital heart defect phenotype. Conclusions: CNGen is the first published software for the partitioning of copy number genotypes in pedigrees, making possible