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Databases
Genotype
likelihoods Validation
A getting started guide for FamLink2 (version 2.3 and above) is
available through https://famlink.se/getting_started_famlink2.pdf.
For getting started in FamLink 1.16 and below,
see text below.
This is a description of how FamLink can be
used to calculate the LR for a case involving two linked markers and the
hypotheses H1: “grandparent - grandchild” versus H2:”Unrelated”. Genetic
data for a child and the alleged grandchild exist. (Below you are guided to
provide input in a way which allows for the result to be checked against a
theoretical result in the paper by Kling, Egeland and
Tillmar, 2012). 1. Open FamLink.
2. Click on the “Frequency database” option in the File menu. 3. Click the “Option” tab. The ‘Error rate’ should be set to 0 and ‘Theta(r)’ to 0.1. 4. Save and close the “Frequency database” option and
click on “New wizard” in the File menu. 5. Select the “Grandparent” pedigree
as the basic hypothesis and click “next”. (There are several similar pedigrees
and you should choose the one with the precise text ‘Grandparent’ under). 6.
Choose “Unrelated man” in the next dialog as the alternative hypothesis. Move
on by clicking “next”. 7. First select “1.NN”, which corresponds to the
alleged grandparent, and enter the DNA-data by using the drop down menu. Select
the first allele in the drop down menu in all cases. Next select “2.NN” and
assign alleles which differ from those of the first individual for instance by
selecting the second allele in the drop down menu in all cases. 8. Click
next and click on the “Calculate” tab. The likelihood for the hypotheses, and
the corresponding LR, is calculated. When you click on ‘Grandparent’ pedigree
you should see the output LR(Linkage): 0.45 LR(No
linkage): 0.25 9. The result can be stored for instance by choosing
‘Generate report’- A more comprehensive description of all the
features of FamLink, and more examples, can be found
in the manual.
You may send comments to daniel.kling@rmv.se