====== PED ======
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**[[http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml#ped|PED]]**\\


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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.

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===== Program information =====
  * written in C/C++
  * Mac
  * Windows
  * Unix
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===== Data type handled =====
  * diploid
  * SNP

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===== Input Files =====
  * 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.

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If specially specified following columns can be missing:
  * ''Family ID''
  * ''Individual ID''
  * ''Paternal ID'' and ''Maternal ID''
  * ''Sex''
  * ''Phenotype''

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==== MAP files ====
  * 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). 

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==== Example ====
  * PED files:
<code>
FAM001  1  0 0  1  2  A A  G G  A C 
FAM001  2  0 0  1  2  A A  A G  0 0 
</code>
<code>
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
</code>
  * MAP files:
<code>
1  rs123456  0  1234555
1  rs234567  0  1237793
1  rs224534  0  -1237697 
1  rs233556  0  1337456
</code>

<code>
1    snp1   0   1000
X    snp2   0   1000
Y    snp3   0   1000
XY   snp4   0   1000
MT   snp5   0   1000
</code>
  
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===== How to cite =====
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.