QTDT - Input Files

QTDT takes as input a family data set. For each individual a set of marker genotypes, quantitative phenotypes and covariates may be specified. The data is then analysed with the association model you specify.

QTDT obtains all input data from three files:

File	Description
Pedigree File	Describes family relationships and includes marker genotypes, quantitative phenotypes and covariates. See also the important information on encoding missing data.
Data File	Describes the organization of the pedigree file.
IBD File	List the IBD state probabilities at each marker. These may be calculated an external application such as simwalk2, using the included applications prelude and finale.

Input file names are specified on the command line using the -d (datafile), -p (pedigree) and -i (ibd) options. For example to use the files sibpair.dat, sibpair.ped and sibpair.ibd as input run the command:

  prompt> qtdt -d sibpair.dat -p sibpair.ped -i sibpair.ibd

The -x option is used to specify the missing value code.