Difference between revisions of "consang"
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Latest revision as of 14:04, 22 April 2016
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This part explains the concepts of consanguinity and relationship used by GeneWeb and how they are computed. The algorithms of consanguinity and relationship were written by Didier Rémy, director of research at INRIA. We thank him for that.
Consanguinity and Relationship
The genom of an individual consists of a great number of genes which, if mutations are ignored, reproduce identically. The genes can be used to measure the identity of a person. The genes are placed in precise locations named “locus”. Each individual has for each locus two genes, one transmitted by his mother, the other by his father, and transmits to his children a copy of the one of his genes.
The Consanguinity of an individual x is the probability cg(x) to find in a given locus two identical genes.
The Relationship of two individuals x and y is the probability pr(x, y) to find in the same locus two identical genes.
The command consang will compute consanguinity in a GeneWeb base.
Display of consanguinity level for each individual is optional and controlled by the variable
show_consang= in the
.gwf parameter file.
consang -i dupont
usage: ./consang -i [options] <file_name> -q : quiet mode -i : build the indexes again -scratch : from scratch -mem : Save memory, but slower when rewritting database -nolock : do not lock database.
NB : Option « -i » is mandatory, otherwise indexes will not be recomputed and the base will not perform adequately.
The program executes in seconds or minutes depending on the size of your base, and displays a progress bar.
During computation, querying the base is allowed. If you perform a large number of updates on your base, it is recommended that you perform a consanguinity computation from time to time, which has the added benefit of cleaning the base from unused space resulting from suppressions.
A probability calculus shows that:
- The consanguinity cg(x) is equal to the relationship pr(px,mx) of the parents px and mx of x.
- If x..a..y is a minimal relationship link between x and y (i.e. such as the branches x..a and a..y have just a in common), then it contributes to the relationship of x and y of a factor where n is the length (distance x..a + distance a..y) of the relationship link x..a..y.
The relationship of x and y is the sum of the contributions of all their minimal relationship links.
If the parameter
show_consang= in the
.gwf file allows it, GeneWeb displays the consanguinity and the relationship in the form of a percentage.
Statistically, on the great number of locuses of an individual, the consanguinity corresponds approximately to the percentage of his locuses holding identical genes.
- Albert Jacquard, Genetic structures of the Populations, Masson & Co, 1970.