Hi,
I'm new to BioStar and new to the study of bioinformatics - so I just want to say that I'm incredibly excited to be in a community of bioinformaticians at BioStar.

I've done a google search on Omnibus tests, but there doesn't seem to have a very good explanation of it. I'm just wondering if anyone could explain the concept here? (also, I understand that the F-test is an example of it, but it doesn't really tell me what the umbrella term Omnibus test is).

If you are looking at haplotypes:
In PLINK, an omnibus association test is used to test all haplotypes combined for association with the disease/trait. If association is observed with the omnibus test, a haplotype specific test can then be used to identify which of the specific haplotypes explains the omnibus association, that is, which haplotype is ‘driving’ the association.

An F test tests a model which may have multiple explanatory variables contributing to the variance explained by the model. An F test is an omnibus test because the significance of the model is a measure of the overall significance of the explantory variables and the way they are combined, not the individual variables by themselves. Let's say I want to model how long a hamster can do the tango. My model contains "weight" and "age" as additive explanatory variables. The F test returns the significance of both of these together, even if in reality the only significant contributor is age. There is a good explanation on the wikipedia page for F-test in the "Multiple-comparison ANOVA problems" section.

Another good example of an omnibus hypothesis test is the chi-square test for categorical data. Taking independence of the categorical variables as the null hypothesis, a significant result only tells you that independence is improbable, but does not yield any information about which levels are significantly different.

I think of omnibus tests as analogous to existence proofs: they'll confirm there's something there, but won't tell you what it is.

Maybe someone in http://stats.stackexchange.com will be able to answer.