PED
The “ped” file format refers to the widely-used format for linkage pedigree data and used as input for the program PLINK. PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.
Family ID
Individual ID
Paternal ID
Maternal ID
Sex
(1=male; 2=female; any other character=unknown)Phenotype
(only 1 phenotype! The phenotype can be either a quantitative trait or an affection status column: PLINK will automatically detect which type (i.e. based on whether a value other than 0, 1, 2 or the missing genotype code is observed))#
0
If specially specified following columns can be missing:
Family ID
Individual ID
Paternal ID
and Maternal ID
Sex
Phenotype
FAM001 1 0 0 1 2 A A G G A C FAM001 2 0 0 1 2 A A A G 0 0
1 1 0 0 1 1 A A A A A A A A A A 2 1 0 0 1 1 A C A C A C A C A C 3 1 0 0 2 1 A A A A A A A A A A 4 1 0 0 2 1 A C A C A C A C A C
1 rs123456 0 1234555 1 rs234567 0 1237793 1 rs224534 0 -1237697 1 rs233556 0 1337456
1 snp1 0 1000 X snp2 0 1000 Y snp3 0 1000 XY snp4 0 1000 MT snp5 0 1000
Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, Bender D, Maller J, Sklar P, de Bakker PIW, Daly MJ & Sham PC (2007) PLINK: a toolset for whole-genome association and population-based linkage analysis. American Journal of Human Genetics, 81.