Format of Pedigree File

The following description is adapted from Linkage User's Guide.

Default Name:  "pedfile.dat"

This file describes the pedigree (s).
Each line in the file describes an individual in one of the pedigrees.

Column 1: Pedigree number
Column 2: Individual number
Column 3: Number of father
Column 4: Number of mother
Column 5: Number of first child
Column 6: Number of next sibling with same father
Column 7: Number of next sibling with same mother
Column 8: Sex - (1 = Male, 2 = female)
Column 9: ignored (the value must be 0)
Column 10 -> : Phenotypic data for the loci being analyzed.  The Phenotype data differs according to the locus type (the possible locus types are described below).

For an affection status type locus:

In the first column appears the disease status, where:
0   =  unknown
1   =  unaffected
2   =   affected
In the second column appears the penetrance class that this person belongs to  (if there's more than 1 penetrance class).  If there is only one penetrance class, the phenotype includes only the disease status.
For a numbered alleles type locus:
There are 2 columns which hold the alleles of the person for this marker. An unknown phenotype is coded as 0 0.
For sex-linked loci, males have a single allele. With the allele 1, for example, the phenotype can be coded 1 0 or 1 1.
For a complex affection type locus (this type of locus doesn't exist in Fastlink):
There will be one phenotype description that corresponds to all the complex affection loci.  This phenotype description is the same as for an affection status type locus.

Back To Superlink's web-page