This lab will cover only one small MORGAN program, kin, which computes the kinship coefficient between specified pairs of individuals, and the inbreeding coefficient of specified individuals.
If using the Biostat linux computers:
Remember that if you did not discover how to put the source ~statgen/.statgen.cshrc
into your own .cshrc (or equiv.) file, you will need to give this command each time you log on, to access the statgen programs.
To run kin you will need a parameter file and a pedigree file. These files can be found in the IBD subdirectory of the MORGAN_Examples that come with the tutorial. Alternatively, you may find these files here:
To run the program kin on the example file, type:
% kin jv_rep_kin.par
or, if you would like to send your output to a file, such as kin.out, type
% kin jv_rep_kin.par > kin.out
or, if you decided to call the pedigree file something different such as my-pedfile
% kin kin.par ped my-pedfile
(The ped key on the command line overrides whatever is in the parameter file.)
Look at your output, or output file. It should be self-explanatory.
Practice modifying the jv_rep_kin.par file to calculate an inbreeding coefficient or kinship coefficient for another individual or pair of individuals. Apparently, kin thinks it is an error to try to compute a kinship of an individual with itself: I need to fix this, but it is not yet fixed!! .
Also note that for your single-component pedigrees you just leave out the component 1 bit of the statement. You can ask for any number of pairs for kinship in one statement (as the two pairs in the example), and any number of individuals for inbreeding (as the two in the example). You should have (for each component if you have more than 1), just one kinship request statement and just one inbreeding request statement in your parameter file.
Your output should include the following:
(i) Calculations of the kinship coefficients between members of four pairs of individuals in your pedigree. Try to find pairs with different kinship coefficients, or with different relationships having the same kinship coefficient. At most one of your pairs should have kinship coefficient 0, and at least one of the pairs should be a pair of bilateral relatives other than siblings.
(ii) Calculations of the inbreeding coefficients for three non-founder individuals in your pedigree. At most one should have inbreeding coefficient 0. Try to find individuals with different inbreeding coefficients if you have them.
Turn in a sheet of paper with your results, with brief explanation of the relationships between the individuals you have chosen (for kinship) or between their parents (for inbreeding).