QTDT - Pedigree File

The format of the pedigree file is a superset of the commonly used pre-makeped LINKAGE format. Each line in the pedigree file has the following format:

  <famid> <pid> <fatid> <motid> <sex> <additional data>

Columns should be separated by spaces or tabs. The first five columns describe family relationships, and have the following format:

Column	Description
famid	Family Identifier. A unique identifier for each family consisting of alphanumeric characters only.
pid	Personal Identifier. A unique alphanumeric identifier for each individual within a family.
fatid, motid	Parental Identifiers. Specify the parents for this individual. Either both parents or none must be present in the pedigree file.
sex	Sex Code. A single character sex code. Should be 1 or M for males, 2 or F for females and 0 or X if missing.

None of the above identifiers are case-sensitive. Additional columns are described in the data file section of this document.

A sample pedigree file, including a quantitative trait, two marker genotypes and a single covariate might read:

  1000 1 0 0 1  1.87  1/2 2/2  40
  1000 2 0 0 2  1.65  1/2 1/1  38
  1000 3 1 2 1  1.80  1/1 1/2  20
  1000 4 1 2 1  1.75  2/2 1/2  17
  (...)

In this case individuals 3 and 4 (in family 1000) are both male and listed as the offspring of 1 and 2. The '/' (forward slash) in the marker genotypes is optional and spaces may be used instead. The corresponding data file might look like this:

 T    HEIGHT
 M    GH1_SNP132
 M    GH1_SNP146
 C    AGE

Missing Values

By default, QTDT considers all non-numeric text values in Trait and Covariate columns of the pedigree file to represent missing values.

If you wish to use a numeric code, such as -99.999, to specify missing values use the -x option. All numbers in Trait or Covariate columns matching this value exactly will be considered missing values. Caution is obviously recommended when this option is used, as misinterpretation of the missing value code could cause unexpected results.

For example, the following command line specifies that the pedigree file mydata.ped (corresponding to datafile mydata.dat) uses -99.999 to encode missing values:

  prompt> qtdt -d mydata.in -p myped.in -x-99.999

Twin data

Please see the twins section.