Thursday, July 24, 2014

PLINK file formats: .map / .ped

Source: PLINK Flat files (MAP/PED) « GWASpi

MAP files

The fields in a MAP file are:

  • Chromosome
  • Marker ID
  • Genetic distance
  • Physical position
Example of a MAP file of the standard PLINK format:
21 rs11511647 0 26765
X rs3883674 0 32380
X rs12218882 0 48172
9 rs10904045 0 48426
9 rs10751931 0 49949
8 rs11252127 0 52087
10 rs12775203 0 52277
8 rs12255619 0 52481

PED files

The fields in a PED file are

  • Family ID
  • Sample ID
  • Paternal ID
  • Maternal ID
  • Sex (1=male; 2=female; other=unknown)
  • Affection (0=unknown; 1=unaffected; 2=affected)
  • Genotypes (space or tab separated, 2 for each marker. 0=missing)
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Example of a PED file of the standard PLINK format:
FAM1NA06985 0 0 1 1 A T T T G G C C A T T T G G C C
FAM1 NA06991 0 0 1 1 C T T T G G C C C T T T G G C C
0 NA06993 0 0 1 1 C T T T G G C T C T T T G G C T
0 NA06994 0 0 1 1 C T T T G G C C C T T T G G C C
0 NA07000 0 0 2 1 C T T T G G C T C T T T G G C T
0 NA07019 0 0 1 1 C T T T G G C C C T T T G G C C
0 NA07022 0 0 2 1 C T T T G G 0 0 C T T T G G 0 0
0 NA07029 0 0 1 1 C T T T G G C C C T T T G G C C
FAM2 NA07056 0 0 0 2 C T T T A G C T C T T T A G C T
FAM2 NA07345 0 0 1 1 C T T T G G C C C T T T G G C C

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