Pedigree MAP File Format:
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.