Pedstats Tutorial -- Per Marker IBD Information
Since there are a finite number of alleles at most genetic loci, individuals may exhibit the same
genotype at a particular locus but, nevertheless, carry distinct chromosomes. Information on allele frequencies and neighbouring
markers can be used to estimate the probability that any two individuals actually inherited the same chromosome
from founders in the pedigree.
A convenient way to summarize IBD sharing information is to list pairwise sharing information for relative pairs
in an IBD file, where each line has the format:
<family> <person1> <person2> <marker> <z0> <z1> <z2>
and <z0>, <z1> and <z2> denote the probability that <person1> and
<person2> in <family> share 0, 1 or 2 alleles IBD at the marker locus
IBD files can be created by programs such as MERLIN for use by programs like QTDT. When an IBD file
is supplied as input (using the -i command line option), PEDSTATS verifies that it includes IBD information for all
families in the pedigree file and for each marker locus, will list the total number of families that have some IBD
sharing information provided.
As an illustration, we'll rerun our basic analysis using the same pedigree and
data files but also specify a corresponding ibd_file using the -i command line option.
pedstats -p basic3.ped -d basic3.dat -i basic3.ibd
With the ibd file supplied as input, you should get an additional
section of text output after the section summarizing marker information:
IBD FAMILY INFORMATION (FROM FILE)
[Singletons] [Trios] [2 generations] [3+ generations]
some_marker 0/0 0/0 0/0 2/2
NOTE: All counts are number of families per category that have some
marker IBD information available.
This table summarizes the number and types of families listed in
the ibd file that have some
ibd information at the marker some_marker. From this, you should
be able to verify that there was ibd information for the locus
some_marker supplied for 2 families and that each of these families had
three or more generations. Note as well, that the information supplied in the ibd
file doesn't need to be complete; in our example file ibd
information was incomplete for family 2, but since some information
was available for that family, it was counted in the overall tally of families.
For further information on IBD estimation and IBD file formats, see the QTDT or MERLIN documentation.