Examples of kinship and gene ibd at linked loci. Programs
autolink and sim_ibd_link
As for the previous lab, these are MORGAN programs but of a primitive form.
autolink is a generalization of kin. It uses recursion to
compute two-locus inbreeding -- the probability that the two haplotypes of
an individual are ibd at both of two linked loci. It does this for a
specified number of specified individuals ("probands"), and at a set of
(hard-wired) recombination fractions from 0 to 0.5.
The program sim_ibd_link is as before, but now we use it to look
at patterns of ibd over linked loci -- the example file specifies one
unlinked "trait" locus, and 5 linked "markers", with recombination fractions
0.18, 0.18, 0.1, 0.1. Since we are interested in dependence among the loci
we must score the IBD patterns over the loci. To avoid having too much output,
we just score yes/no (1/0) for some ibd event over windows of loci of a
specified size (3 in the example). The ibd events are ibd/not for the
two haplotypes of an individual (and one can do this simultaneously for
several individuals).
These data are marker data on affected inbred individuals.
The can be used either for
single-marker homozygosity mapping-- which can be done "by hand",
or using Genehunter.
There are also data on 13 markers on chromosome 8 (where the gene is
now known to be). These data provide a useful multilocus
linkage analysis Genehunter example.
Info from Fall 2000
This should all still work, but the above will be easier for those not
so computer literate!
Some files are given as compressed tar file (.tgz). To open .tgz
files, say something like
aleph% tar zxvf ghexample.tgz
A new directory will be created with those files.
Last updated: Monday, 28-Nov-2005 14:56:37 PST
