tutorial
the files
Your own data can be used to test the GDF, but since it has plenty of options available we have built an appropriate data set that will highlight the most relevant ones. In order to follow this tutorial we encourage you to download our demo data file, configuration file and pedigree file. The data on them contained is fictitious, built for this tutorial as an example of data that would come from both Sequenom and SNPlex, respecting each platform output file format, and using a random pedigree information. The lines that begin with the "#" sign in the data file are our informative tags.
the load
Enter the configuration, data and pedigree files in the boxes using the appropriate "browse..." buttons. GDF will complain if the first box is not filled, but it will allow you to continue if you do not fill the other ones as they are optional.
the options
You may now select or deselect the checkboxes according to what you would like to do with your data. We would suggest you to select all possible program inputs to obtain the most complete output, and to leave the rest of the options with the default values.
the results
You will see a complete report on the screen of what the program has done. Different sections will give you information about what GDF found: genes and snps unused, unknown snps, failed samples and snps, and some other features. Some statistics summarizing the most relevant genotyping features are displayed at the bottom, and you will be able to click at the very bottom of the page on the link that will let you download the zip file that contains all the results.