LINKAGE pedigree format

PED is a white-space (space or tab) delimited file, the first six columns are mandatory:

• Family ID: A unique identifier for this individual's family. Unrelated individuals should not share a family ID.
• Individual ID: An identifier for this individual. Should be unique within his family (see above).
• Father's ID: Identifier corresponding to father's individual ID or "0" if unknown father.
• Mother's ID: Identifier corresponding to mother's individual ID or "0" if unknown mother.
• Sex: Individual's gender (1=male, 2=female).
• Affection status: Affection status to be used for association tests (0/NA=unknown, 1=unaffected/case, 2=affected/control).

A standard LINKAGE Pedigree format typically does not include a header line; the first line is expected to represent the first individual rather than the column names. However, we do allow the use of a PED file with header information.

==! CAUTION== If a header is present, it must start with fid iid(names for the first two columns; case insensitive). Failure to adhere to this rule may result in the program interpreting the first row as an individual information line. There is an example:

fid    iid    fatid    matid    sex    disease    QT    age
1084    1084    0    0    1    1    88.32    87
1086    1086    0    0    2    2    85.52    80
1087    1087    0    0    2    2    78.66    77
23    2344    2347    2348    1    1    94.05    NA
23    2347    0    0    1    0    87.54    40
23    2348    0    0    2    2    NA    36