PED

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.

• written in C/C++
• Mac
• Windows
• Unix

• diploid
• SNP

• whitespace (spaces and or tabs) separated text file *.ped
• each line correspond to one individual
• following first 6 columns are mandatory (The IDs are alphanumberic):
  • 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))
• Comments: line starts with #
• Affection status, by default, should be coded:
  • -9 missing
  • 0 missing
  • 1 unaffected
  • 2 affected
• column 7 onwards: Genotypes
  • any character (e.g.: 1,2,3,4 or A,C,G,T or anything else)
  • missing genotype: 0
  • all markers must be biallelic (diploid). Either both alleles should be missing or neither. Haploid data: encode them as diploid homozygot. Two alleles are shown after each other.

If specially specified following columns can be missing:

• Family ID
• Individual ID
• Paternal ID and Maternal ID
• Sex
• Phenotype

• Each line of the MAP file describes a single marker and must contain exactly 4 columns:
  • chromosome (1-22, X, Y, MT or 0 if unplaced)
  • rs# or snp identifier
  • Genetic distance (morgans) (missing: 0)
  • Base-pair position (bp units) (Base-pair positions are expected to correspond to positive integers within the range of typical human chromosome sizes)
• The MAP file must contain as many markers as are in the PED file.
• The markers in the PED file do not need to be in genomic order: (i.e. the order MAP file should align with the order of the PED file markers).

• PED files:

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

• MAP files:

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.