STEP-BY-STEP LINKAGE PROGRAMS GUIDE FOR HUMGEN USERS
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THE PEDIGREE FILE
PEDIGREE FILE
This is the file that contains the familial information of the pedigree you are analyzing. Each line represents one individual. Each line has the same number of items (5 or 6), separated by spaces:

  • Line Item 1 - Hyphenated representation of the family and individual (e.g. CA-100 where CA is the family ID and 100 is the individual ID number). Individual IDs must be integers. This family-individual item must be unique in the pedigree file
  • Line Item 2 - The ID number of the individual's father
  • Line Item 3 - The ID number of the individual's mother
  • Line Item 4 - The individual's sex, where 1 = male and 2 = female
  • Line Item 5 - The disease affected status, where 1 = unaffected, 2 = affected, and 0 = unknown
  • Line Item 6 (OPTIONAL) - liability code number usually age-related and specific to the disease in the study

In the example shown to the right, the file name is pCA. The family ID is CA

 CA-027   0   0   1   2
CA-031   0   0   1   1
CA-032   0   0   2   1
CA-104   0   0   2   1
CA-101   027   104   1   1
CA-102   027   104   1   1
CA-103   031   032   2   2
CA-105   031   030   2   2
CA-100   027   104   2   1
CA-030   0   0   2   2

The pedigree file is one of the input files to gtyper2.pl, which creates the .adb and the .pre file. In general, no ABI control lanes are included in the pedigree file because gtyper2.pl will use each line of the pedigree file in the output.adb file. The allele information comes from the Genotyper table.

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Last updated Feb. 3, 2001