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
Family Identifier. A unique identifier for each family
consisting of alphanumeric characters only.
Personal Identifier. A unique alphanumeric identifier
for each individual within a family.
Parental Identifiers. Specify the parents for this individual.
Either both parents or none must be present in the pedigree file.
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:
By default, QTDT considers all non-numeric text values in Trait
and Covariate columns of the pedigree file to represent missing
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
Please see the twins section.