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CNGen v1.0.1 We have created a scritp 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 - 250_thousand_validations.tar.bz2 (md5) 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 - 3_thousand_validations_with_errors.tar.bz2 (md5) 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.
Chip2Spell v1.0 We have created a program that automatically generates the input files for Alohomora_m. The program Chip2Spell takes as input a genotype report and publicly available annotation files and creates the genotype file, map file and frequency file that will be used by Alohomora. The program is especially useful if the map and frequency files for a given plateform are not stored in the Alohomora library, but it is also a quick way to convert the standard Affymetrix or Illumina genotype report format to the AB format requested by Alohomora. The latest Affymetrix and Illumina whole genome plateforms are specifically supported, but it is also possible to use Chip2Spell with previous chips. Chip2Spell was implemented using the perl interpreter version 5.8.8 on a Linux workstation and has been tested on Linux and Widows XP and Vista.
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