We have created a script that converts integrated SNP and CNV calls generated from Birdsuite's Fawkes procedure into phased copy number genotypes (CN genotypes) using familial pedigree data. This software makes possible the use of CNPs and CNVs for genetic linkage with family data. The application is platform independent and may be used by Linux, Windows and Mac users.

It was implemented using the Python interpreter version 2.5.2 on a Linux workstation. CNGen was tested on different Linux distributions, Windows (XP, Vista and 7 RC) and Mac OS/X, using the Python interpreters 2.5.2 and 2.6.1. For now, it doesn't work using Python interpreter version 3.0.1, since there is a dramatic change in the API.

Additional file 1

Archive containing the simulated data for 1 million (out of 3 million) runs on a pedigree containing 47 individuals (14 founders). The archive contains the simulated Fawkes' calls (file validation.fawkes_calls), the partitioned genotyped compute by CNGen and the corresponding log file (file cn_genotype_calls_validation and CNGen.log, respectively) and the pedfile corresponding to the complex pedigree used for simulation (file pedfile.txt). The archive file's size is 72 Mb.

Additional file 2

Archive containing the simulated data for 3 thousand runs with Mendelian errors randomly added. The archive contains the same file structure as the first additional file. The data have been split into three files because of PedCheck's limitations. The archive file's size is 2.2 Mb.

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