Menu
I am currently looking for a piece of software which will be able to map a very large number of GEDCOM files (for around 33,000 individuals) as well as working out ancestral and individual inbreeding coefficients. Does anyone know of any software which is capable????
Thanks
680
In general, for autosomal loci, the inbreeding coefficient for an individual is F = (½)(n1+n2+1), where n1 and n2 are the numbers of generations separating the individuals in the consanguineous mating from their common ancestor. (This formula assumes that the common ancestor is not inbred.)
The term was introduced by Sewall Wright (1922) and is calculated as r = Σ (0.5)L. The calculation considers that at each generation link there is meiosis, i.e., a 0.5 probability that a copy of a particular gene will be passed on to an offspring.
Inbreeding levels of 5-10% will have modest detrimental effects on the offspring. Inbreeding levels above 10% will have significant effects not just on the quality of the offspring, but there will also be detrimental effects on the breed.
Measuring the degree of inbreeding The degree of inbreeding can be measured using a calculation called the coefficient of inbreeding (CoI), or inbreeding coefficient. This calculates the probability that two copies of a gene variant have been inherited from an ancestor common to both the mother and the father.
I don't think you will find any software that does this for you, but it wouldn't be too difficult to write your own. I would take one of the many open source gedcom parsers out there and add the individuals to a graph database such as Neo4j. Once it is in Neo4j, it should be relatively easy to run your calculations on the individuals.
53
If you love us? You can donate to us via Paypal or buy me a coffee so we can maintain and grow! Thank you!
Donate Us With
