INPUT Genotyping Platforms Sequenom SNPlex Illumina Affymetrix*   Generic formats HapMap SNPs vs. Samples tables Samples vs. SNPs tables OUTPUT Association Studies GeneHunter Haploview PLINK MEGA-2 Arlequin Phase Hapblock EMLD Unphased MDR   Population Studies Structure Arlequin Haploview

Table 1: File formats handled by GDF. Being a flexible interface between raw data and specific analysis programs, GDF deals with several input formats coming directly from the genotyping platforms, from the HapMap project, or even from custom made tables. The Affymetrix format coverage is not full though (*), as only general reports may be obtained from it through GDF due to its usual data size, but for the rest of the input formats GDF is able to parse their genotypes and provide the input for several programs of analysis for association and population studies.