04 MAP File Format

Pedigree MAP File Format:

MAP (Links to an external site.) files are tab-separated text files used by the program PLINK, that describe meta-data about each SNP listed in the accompanied PED file.

The four columns are as follows:

  • Chromosome (1-22, X, Y or 0 if unknown)
  • Rs# or SNP identifier
  • Genetic distance along the chromosome (morgans, or centimorgans if specified with the –cm flag)
  • Base-pair position along the chromosome (bp units)

You are allowed three columns (with the genetic distance excluded) if you use the –map3 flag.

Here is an example of 5 SNPs:

1 rs3934834 0 1005806
1 rs9442372 0 1018704
1 rs3737728 0 1021415
1 rs6687776 0 1030565
1 rs9442373 0 1062638

In the above example, all columns were tab-separated. Any base-pair position that is given a negative number means that this SNP should be excluded from any analysis.

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