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:For a numbered alleles type locus:0 = unknownIn 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.
1 = unaffected
2 = affected
There are 2 columns which hold the alleles of the person for this marker. An unknown phenotype is coded as 0 0.For a complex affection type locus (this type of locus doesn't exist in Fastlink):
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.
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.