Question: LD pruning before or after phasing for calculating site frequency spectrum?
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gravatar for Mr Locuace
14 months ago by
Mr Locuace90
Chile
Mr Locuace90 wrote:

I want to calculate the joint-site frequency spectrum (SFS) of 3 populations from phased genotypes generated by Beagle from Plink files). I'd like to know whether it is best to do LD pruning before or after phasing. Also, which LD threshold would be suitable?. I normally remove variants with r2 > 0.2, but I am not sure how this threshold will affect the SFS. Thank you

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