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Genotype
likelihoods Validation
This page contains some Frequently Asked Questions (FAQ).
Q: Can FamLink account for mutations?
A: Yes, for the pre-defined pedigrees we have implemented a slower
algorithm that can handle mutations for linked markers. Please note that
mutations and genotype likelihoods cannot be modeled simultaneously.
Q: Can FamLink handle multiple linked markers?
A: Yes, the software can handle virtually any number of linked markers.
Please keep in mind that LD (allelic association) is not modeled. We recommend
at least 0.5 cM distance between adjacent markers.
Q: Will FamLink provide the possibility to
handle X-chromosomal markers?
A: Yes, in future releases we will extend the software with this option.
X-chromosomal marker can be imported into the software but are currently not
used in any functions/computations.
Q: Will FamLink provide the possibility to
handle Y-chromosomal markers?
A: The software can import any data, but Y-chromosomal data is currently
only used to predict haplotypes.
Q: Can you provide map/freq files for my marker panel?
A: Yes we can assist you with that, please reach out to us. Some databases
are available at the Databases
section.
Q: How do I validate FamLink?
A: A tricky question, head over to the Validation section to get some
hints and suggestions.
Q: Will you do courses?
A: Reach out to us and we may be able to introduce the software.
Q: Is the source code open?
A: The software is freeware, not open source. Having
said that, at special request, the source code can be shared for the purpose of
checking, but not redistributing it.
Q: What programming language is FamLink
written in?
A: 100% C++
Q: Can FamLink use multiple computational
cores (CPU)?
A: Yes, latest version can use up to 22 cores, which can greatly speed
up calculations.
Q: What are the limits of the software?
A: A few limits exist, i) mutations are not completely
handled for all pedigrees, ii) Calculations for STR markers are currently slow,
iii) including several typed samples and extended pedigrees, i.e. beyond second
cousins, can cause the software go out-of-memory.
You may send comments to daniel.kling@rmv.se