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:

Pedigree file

Take a look at

Now take a look at

Finally the program asks for a couple of two-locus inbreeding coefficients, which may or may not be talked about in class. It is just the probability that the maternal and paternal haplotypes of an individual are IBD at both of two linked loci. This probability will depend on the recombination rate between the loci, so the final line specifies the recombination values at which this two-locus inbreeding is to be computed.

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).