Pre-makeped format contains following columns, separated by space and/or tab characters:

    Column 1: Pedigree identifier           { The identifier can be a number
    Column 2: Individual's ID               { or a character string

    Column 3: The individual's father       { If the person is a founder, just put a
    Column 4: The individual's mother       { 0 in each column.

    Column 5: Sex                           { 1 = Male, 2 = Female, Unknown sex is not permitted
    Column 6+: Genetic data                 { Disease and marker phenotypes

Let's assume following pedigree structure (with discrete trait / qualitative phenotype, one liability class) with father, mother, two sons (son1 and son2) and two daughters (dau1 and dau2) with one marker phenotype:

Pedigree	Pedigree symbols
	Affected male Unffected male Affected female Unaffected female

Pedigree structure coded to text file (pre-makeped):

    ped1    father  0       0       1  2   1 2
    ped1    mother  0       0       2  1   1 1
    ped1    son1    father  mother  1  2   1 2
    ped1    son2    father  mother  1  1   1 1
    ped1    dau1    father  mother  2  2   1 2
    ped1    dau2    father  mother  2  1   1 1

Father's and mother's parents are unknown and their id is set to zero (=0) and after sex column is affection status column (disease) where number:

2 means affected
1 means unaffected
0 means unknown

If disease locus has more than one liability class, then liability class column is right after disease. After disease locus column(s) comes marker phenotypes.

using numbers (recommended):

    1       1       0       0       1  2   1 2
    1       2       0       0       2  1   1 1
    1       3       1       2       1  2   1 2
    1       4       1       2       1  1   1 1
    1       5       1       2       2  2   1 2
    1       6       1       2       2  1   1 1

NOTE! Number of spaces between columns does not matter, but if it's formatted as above, it's easy to read. If some individual is not genotyped in some marker, you must enter 0 for each allele (e.g. phenotype = 0 0).

Last line of the file must be empty line!

::: AUTOGSCAN uses pre-makeped LINKAGE format! :::

Post-makeped format comes after above pedigree file is processed with makeped program, which is readable format for LINKAGE (FASTLINK) package and others. See makeped how-to for more info.

LINKAGE format contains following columns:

    Column 1:   Pedigree number
    Column 2:   Individual ID number
    Column 3:   ID of father
    Column 4:   ID of mother
    Column 5:   First offspring ID
    Column 6:   Next paternal sibling ID
    Column 7:   Next maternal sibling ID
    Column 8:   Sex                          
    Column 9:   Proband status (1=proband, higher numbers indicate doubled individuals formed
                                in breaking loops. All other individuals have a 0 in this field.)
    Column 10+: Disease and marker phenotypes (as in the original pedigree file)

Here is above pedigree after it's processed with makeped:

    1 1 0 0 3 0 0 1 1  2   1 2  Ped: ped1  Per: father
    1 2 0 0 3 0 0 2 0  1   1 1  Ped: ped1  Per: mother
    1 3 1 2 0 4 4 1 0  2   1 2  Ped: ped1  Per: son1
    1 4 1 2 0 5 5 1 0  1   1 1  Ped: ped1  Per: son2
    1 5 1 2 0 6 6 2 0  2   1 2  Ped: ped1  Per: dau1
    1 6 1 2 0 0 0 2 0  1   1 1  Ped: ped1  Per: dau2

Makeped recoded pedigree and individual identifiers to numbers and added extra columns. Original pedigree and individual ID's are end of the each line.

Naming of the files (pre-makeped)

It's recommended to have each chromosome in separate file and name files according to chromosome as chr1.raw, chr2.raw,...,chr22.raw.

Documentation and for more info

Handbook of Human Genetic Linkage, Joseph D. Terwilliger and Jurg Ott. Johns Hopkins University Press, Baltimore (1994)