compatibility
supported genotyping platforms
GDF is able to work with any data coming from Sequenom, SNPlex, Illumina, Affymetrix (targetted genotyping and mapping arrays), Taqman, HapMap, and tables of snps versus samples (or samples versus snps). And since it automatically detects the format line by line, you can use more than one platform at the same time.
available output formats
The use of GDF directly depends on the analysis programs used afterwards to process the data. The number of output formats that GDF may provide is not supposed to be fixed, but to grow with the needs of the researchers (please feel free to contact us requesting any format you may need to be included on that list). The programs currently supported are Arlequin (some manual edition yet needs to be done with on the file header), Phase - EMLD - HapBlock (same input shared), GeneHunter - Haploview - Unphased (same input shared too), MDR and Structure.
Additionally, the LGEN data format can be generated combining the raw data with a PED file, in order to feed analysis software such as PLINK. The MAP file may be also generated for Affymetrix data, either for Targetted Genotyping or Mapping arrays, if the corresponding reduced annotation files is provided as the "translation for alleles" file. This reduced files should be generated by running the RAFA program in the same directory as the raw compressed annotation files.
operating systems
This program has been written in perl, and so it can be locally run on the command line of any OS for which a perl interpreter has been developed. In addition, a graphical user interface has been developed for Windows platforms and it is distributed along with the program executable. In case the windows graphical GDF reports a runtime error at startup, it may be a problem with the .NET framework installed on your computer. You may download the latest .NET framework from Microsoft here.