What is “ped” file format?
The “ped” file format refers to the widely-used format for linkage pedigree data. Each line describes a single (diploid) individual in the following format: family_ID individual_ID father_ID mother_ID gender phenotype genotype_1 genotype_2 … If your data lacks pedigree information (for example, unrelated case/control individuals), set the father_ID and mother_ID to 0. sex denotes the individual’s gender with 1=male and 2=female. phenotype refers to the affected status (for association studies) where 0=unknown, 1=unaffected, 2=affected. Finally, each genotype is written as two (=diploid) integer numbers (separated by whitespace), where 1=A, 2=C, 3=G, 4=T. No header lines are allowed and all columns must be separated by whitespace. Check out the information at the PLINK website on the “ped” file format.
