the options
the running options
The "Deal with reversed tables" option allows to work with data in tables with information of one sample per input line, as GDF expects information of one snp per input line by default.
The "Remove samples with some ungenotyped snps" option allows you not to include samples in the output files in which snps that were genotyped on other samples were not tested, for the same gene or group defined in the snp configuration file. Note that this option is by default unselected, and so the untested snps will reflect failed genotypes.
The "Remove samples without pedigree" and "Remove samples without population" options are only available when a pedigree or population files are used respectively, and allows not to include samples in the output file that are not present in these pedigree or population files. By default this samples are removed, but if included they will be assigned default values (unknown population if appropriate, and additive numeric pedigree label, males, orphans, and no affectation status in the pedigree file case).
The "rs prefix adding" option allows you to use numeric code snps instead of their entire 'rs' code in the input file. It is selected by default, what will lead to format any numeric snp code with the adding of a 'rs' prefix.
There are two debugging options more available, that will print on the screen the lines that have not been processed because of their content, and also the lines that have not been recognized because of their format.
the output formats
All program outputs are unselected by default, but you are able to modify these settings as you may want. Note that you will only be able to obtain the MDR output if a pedigree file with case-control information is used, and that you will only be able to select the outputs for population studies if a population file is entered.
Formatting your data is not mandatory to run GDF. In fact, it can be used without selecting any of these options, and it will still run the error checking and the statistics engine.