RelativeFinder - Revision history

Goncalo: /* Current Limitations and Todo List */

2010-11-23T08:17:54Z

Current Limitations and Todo List

← Older revision		Revision as of 08:17, 23 November 2010
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	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 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 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.

Goncalo: /* Current Limitations and Todo List */

2010-08-13T17:18:57Z

Current Limitations and Todo List

← Older revision		Revision as of 17:18, 13 August 2010
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	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 looks for a pair of files called ''testCases.dat'' and ''testCases.ped'' in the current working directory. This pair of files specifies alternate relationships to be considered.

	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.		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.

Goncalo: /* Download */

2010-08-13T17:18:27Z

Download

← Older revision		Revision as of 17:18, 13 August 2010
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	== Download ==		== Download ==

	A source package is available for download from [http://www.sph.umich.edu/csg/abecasis/downloads/generic-relativeFinder-2010-08-12.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 ==

Goncalo: /* Command Line Options */

2010-08-12T21:08:43Z

Command Line Options

← Older revision		Revision as of 21:08, 12 August 2010
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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''

Goncalo: /* Download */

2010-08-12T21:07:29Z

Download

← Older revision		Revision as of 21:07, 12 August 2010
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	== 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-2010-08-12.tar.gz here].

	== Current Limitations and Todo List ==		== Current Limitations and Todo List ==

Goncalo: /* Alternative Relationships */

2010-08-12T21:06:41Z

Alternative Relationships

← Older revision		Revision as of 21:06, 12 August 2010
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	== 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'''
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	</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 ==

Goncalo: /* How It Works */

2010-06-15T05:30:27Z

How It Works

← Older revision		Revision as of 05:30, 15 June 2010
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	'''relativeFinder''' examines every pair of genotyped individuals in a pedigree. Then, it calculates the likelihood of the pair of the observed genotype data for the pair using the relationship specified in the pedigree and using a series of alternate relationships (described in a template pedigree file). If any of these alternate relationships makes the observed genotype data more likely, the pair is flagged.		'''relativeFinder''' examines every pair of genotyped individuals in a pedigree. Then, it calculates the likelihood of the pair of the observed genotype data for the pair using the relationship specified in the pedigree and using a series of alternate relationships (described in a template pedigree file). If any of these alternate relationships makes the observed genotype data more likely, the pair is flagged.

			Before evaluating relationship likelihoods, relativeFinder will flag individuals with outlier patterns for heterozygosity or missing genotypes. To do this, relativeFinder checks whether the fraction of heterozygous sites or the total number of available genotypes differs froom the sample average by three standard deviations or more. Results for any flagged samples should be treated with caution, as problematic heterozygosity or missing data patterns can lead to odd results for the relativeFinder algorithm.

	== Command Line Options ==		== Command Line Options ==

Goncalo: /* Download */

2010-06-15T05:27:23Z

Download

← Older revision		Revision as of 05:27, 15 June 2010
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	== Download ==		== Download ==

	A source package is available for download from [http://www.sph.umich.edu/csg/abecasis/downloads/generic-relativeFinder-2010-05-20.tar.gz here].		A source package is available for download from [http://www.sph.umich.edu/csg/abecasis/downloads/generic-relativeFinder-2010-06-15.tar.gz here].

	== Current Limitations and Todo List ==		== Current Limitations and Todo List ==

Goncalo: /* Alternative Relationships */

2010-05-20T04:16:06Z

Alternative Relationships

← Older revision		Revision as of 04:16, 20 May 2010
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	'''Example of testCases.dat file'''		'''Example of testCases.dat file'''
	<source>		<source lang="text">
	Z zygosity		Z zygosity
	</source ~~lang="text"~~>		</source>

	In this case, the data file simply indicates that the five canonical columns in the pedigree (family id, individual id, father, mother and sex) will be followed by a column indicated whether individuals are MZ twins.		In this case, the data file simply indicates that the five canonical columns in the pedigree (family id, individual id, father, mother and sex) will be followed by a column indicated whether individuals are MZ twins.

Goncalo: /* Alternative Relationships */

2010-05-20T04:15:23Z

Alternative Relationships

← Older revision		Revision as of 04:15, 20 May 2010
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	<source>		<source>
	Z zygosity		Z zygosity
	</source>		</source lang="text">

	In this case, the data file simply indicates that the five canonical columns in the pedigree (family id, individual id, father, mother and sex) will be followed by a column indicated whether individuals are MZ twins.		In this case, the data file simply indicates that the five canonical columns in the pedigree (family id, individual id, father, mother and sex) will be followed by a column indicated whether individuals are MZ twins.

	'''Example of testCases.ped file'''		'''Example of testCases.ped file'''
	<source>		<source lang="text">
	MZTWIN 1 0 0 1 0		MZTWIN 1 0 0 1 0
	MZTWIN 2 0 0 2 0		MZTWIN 2 0 0 2 0