2.3 File identification statements

Within the parameter file, file names are delimited with single or double quotation marks (` or "). File names submitted on the command line are not delimited with quotation marks. In a parameter file, either of the two statements below would identify `pedchk.ped' as the pedigree file to be read.

input pedigree file "pedchk.ped" input pedigree file `pedchk.ped'

The most commonly used file identification statements are:

input pedigree file filename

The input pedigree file is required for most programs and may be specified either in the parameter file or through command line options.

output [overwrite] pedigree file filename

The output pedigree file is required by genedrop. Other programs also check for errors in the pedigree. If there are errors that the program is able to correct or if there are requested changes to the pedigree file format, the new pedigree data is written to this file.

input marker data file filename

Marker data, such as marker allele frequencies, map distances between markers and individuals' genotypes, can be included in the parameter file itself or in a separate file, called the marker data file. This statement is used when the marker data are not included within the parameter file. The marker file contains the `set marker data' statements. Marker data are used by Autozyg programs. See Autozyg computational parameters.

input seed file filename

This file contains statements to set random seeds for the Monte Carlo based programs. The seed file may contain multiple lines (as in the case when the input seed file is also used for the output seed file). If so, the seeds in the last line override previous ones (with warnings issued). If no seed file is named on the command line or in a parameter statement and there are no statements to set random seeds in the parameter file, default seeds (12345, 1073 (hexadecimal 0x3039, 0x431)) are used.

output [overwrite] seed file filename

The final random seeds are saved if an output seed file is named. This file could be the same as the input seed file. New entries are appended to the old file.