the first few columns are identical to the pre-MAKEPED file

col 1: pedigree ID
col 2: person ID
col 3: father ID
col 4: mother ID

three extra columns generated by MAKEPED

col 5: first offspring ID
col 6: next parental sibling ID
col 7: next maternal sibling ID

back to pre-MAKEPED file:
col 8: gender (1 for male, 2 for female)

one more extra column generated by MAKEPED (total 4 extra columns)

col 9: proband status (related to the "leading person" and 
      "loop breaking" persons in the pedigree. otherwise 0)

back to pre-MAKEPED file:
col 10: affection status

the next column is optional (be careful! since you don't
know whether you have this column or not until you check
the LINKAGE parameter file): the liability class this person
belongs to.

the rest are the marker information. note that one marker
contributes two columns, for both parents, although it
is not clear which one is from father and which is from 
mother.  the coding of the marker allele values is
arbitrary as long as it is consistent.