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; -d ''datafile'' -p ''pedigreefile'' -m ''mapfile''
; -d ''datafile'' -p ''pedigreefile'' -m ''mapfile''
: A set of required input files in [http://www.sph.umich.edu/csg/abecasis/Merlin/tour/input_files.html Merlin format]. These files list the individuals to be evaluated. It is recommended that a whole genome worth of data should be available.
: A set of required input files in [http://www.sph.umich.edu/csg/abecasis/Merlin/tour/input_files.html Merlin format]. These files list the individuals to be evaluated. It is recommended that a whole genome worth of data should be available.
; -t ''testRelationshipData'' -q ''testRelationshipPedigree''
: An optional set of files, also in Merlin format, that describe relationships to be considered by RelativeFinder.
; -f ''alelleFrequencyModel''
; -f ''alelleFrequencyModel''
== Alternative Relationships ==
== Alternative Relationships ==
The set of relationships to be considered by relative finder is described in a pair of merlin format data and pedigree files. Here is what they might looi like:
The set of relationships to be considered by RelativeFinder can be specified in a pair of merlin format data and pedigree files. Names for these files can be specified with the '''-t''' (for the data file) and '''-q''' (for the pedigree file) command line options. Within this pedigree, each family should describe one potential relationship. The placement of the individuals within the test pedigree should be labeled with the words "TEST1" and "TEST2".
If these files are not available, RelativeFinder will consider a basic set of relationships for each pair of individuals (siblings, half-siblings, identical twins, parent-offspring pairs, unrelated individuals, or an avuncular relationship).
Here files specifying relationships to be considered might look like:
'''Example of testCases.dat file'''
'''Example of testCases.dat file'''
</source>
</source>
In this case, the pedigree describes 6 alternate relationships (identical twins, siblings, half-siblings, avuncular pairs, parent-offspring pairs and unrelated individuals). In each putative relationship, the placement of the individuals being evaluated is indicated by the TEST1 and TEST2 tags.
In the example above, the pedigree describes 6 alternate relationships that match the default relationships considered by RelativeFinder(identical twins, siblings, half-siblings, avuncular pairs, parent-offspring pairs and unrelated individuals). Note that, for each putative relationship, the placement of the individuals being evaluated is indicated by the TEST1 and TEST2 tags.
== Download ==
== Download ==
A source package is available for download from [http://www.sph.umich.edu/csg/abecasis/downloads/generic-relativeFinder-2010-06-15.tar.gz here].
A source package is available for download from [http://www.sph.umich.edu/csg/abecasis/downloads/generic-relativeFinder-2010-08-13.tar.gz here].
== Current Limitations and Todo List ==
== Current Limitations and Todo List ==
The current implementation does not include support for X linked markers and should only be used with autosomal markers.
The current implementation does not include support for X linked markers and should only be used with autosomal markers.
The current implementation simply reports the most likely relationship and the difference in log-likelihood between this relationship and the originally specified relationship. It would be better to use an E-M algorithm to calculate a prior probability for each relationship and to only report as problematic pairs where the posterior probability of a mis-specified relationship is high.
The current implementation simply reports the most likely relationship and the difference in likelihood between this relationship and the originally specified relationship. It would be better to use an E-M algorithm to calculate a prior probability for each relationship and to only report as problematic pairs where the posterior probability of a mis-specified relationship is high.
