how to set up same detected regions between omegaplus and SweeD

[魏凯]

Hi all,

I am running omegaplus and sweed to detect positive selection sweeps. I wish to get some overlaps between them. But they have different length in every regions. For example, for chr1, I have same grid 1000 between omegaplus and sweed, the results showed me the positions is similar, but the start position and end position is different they detected. So, can anyone give a good idea to solve this problem? I wish to detect Omega and CLR in same regions. thanks a lot!  

best,

Kai

[Nikolaos Alachiotis]

Hi Kai,

When you say that "the start position and end position is different", do you refer to the reported regions per grid point by both tools?

These are definitely going to differ since the tools implement different statistics and stop criteria in the search for the max score per location.The evaluated locations (grid points) are the same between both tools.

If you want to detect the points that both tools agree on, you can use the grid locations and check those.

Pavlos has a written a detailed description for this here:

http://pop-gen.eu/wordpress/selective-sweep-analysis-pipelines/combine-omegaplus-and-sweed-thresholds-from-simulations

Regards,

Nikos

 

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Nikolaos Alachiotis