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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''
== 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.
