3.3 Running pedcheck examples

Examples for the program pedcheck are under the subdirectory `Pedcheck/'. The commands using example files are listed below. Have a look inside the pedigree and parameter files, then verify that the output files are as you would expect them to be. If error messages are generated, verify that they make sense and see if you can make the necessary corrections so that pedcheck will run.

./pedcheck check.par

runs on input pedigree file `check.ped'. The pedigree contains no errors, but has no gender specified and is not in chronological order. Look at the parameter file: you will see that it specifies the absence of gender, and requests that gender be assigned and that the output pedigree be chronologically ordered. Then, indeed, the output pedigree file `check.oped' has gender assigned and has the members reordered. Notice that individuals who are not parents (531 and 541) have missing gender, `0', in the fourth column of `check.oped'. You will get an error message and the program will quit if `check.oped' already exists. If this occurs, delete the file and try again or use another output file name.

./pedcheck imp.par

runs on input pedigree file `imp.ped'. The pedigree contains an individual who is his own ancestor.

./pedcheck empty.par ped sex.ped

runs with an empty parameter file, with input pedigree file `sex.ped' specified on the command line. What does the output say is wrong with this pedigree?

./pedcheck empty.par ped dup.ped

runs with an empty parameter file, with input pedigree file `dup.ped' specified on the command line. What does the output say is wrong with this pedigree?