PLINK Flat files (MAP/PED)

PLINK is a very widely used application for analyzing genotypic data. It can be considered the “de-facto” standard of the field, although newer formats are starting to be widespread as well.
The standard PLINK format description can be accessed from their official site over at their site

The standard PLINK fromat provides sufficient information for a straight-forward association study. You may use the sex and affection fields for GWASpi to perform GWS studies. Optionally, if you want to provide the additional data fields that GWASpi supports, you may chose to use the Sample Info & Phenotype format. If you do so, the information provided in this file will take precedence to the one provided in the PED file!

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)
Example of a PED file of the standard PLINK format:
FAM1 NA06985 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