Using monomorphic sites as input in OmegaPlus

[Joe Colgan]

Hi, 

I am interested in using OmegaPlus to identify sweeps within a natural population of haploid individuals. 

As I'm interested in identifying complete sweeps (i.e. present within all individuals within the population), is there a means of using monomorphic sites within the input for OmegaPlus? There doesn't appear to be an option (-monomorphic) like there is in SweeD. 

Any help you can provide is greatly appreciated. 

Kind regards, 

Joe

[Nikolaos Alachiotis]

Hi Joe,

There is no way to use monomorphic sites with OmegaPlus. OmegaPlus implements the omega statistic which relies on LD. Monomorphic sites
will inflate LD values and wont let the omega statistic operate as intended.

Regards,

Nikos

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Nikolaos Alachiotis