Unused genes Genes present in the configuration file with all their SNPs untested Unknown SNPs SNPs present in the data file but not in the configuration file Untested SNPs SNPs present in the configuration file but not in the data file Failed SNPs SNPs that failed in all the genotyped samples Failed samples Samples with no successful genotype No pedigree samples Samples with no pedigree information present in the pedigree file if used Unperformed tests samples SNPs that were not genotyped on a sample but they were tested on the rest Overlapping information samples Samples that carry a third allele, assuming most genotyping techniques deal with bi-allelic SNPs

Table 2: Analyses performed by GDF. A description of the internal checks that GDF performs in order to improve the description of the data being analysed, which are given at the end of each run.