Question: LD pruning before or after phasing for calculating site frequency spectrum?
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gravatar for Mr Locuace
18 months ago by
Mr Locuace100
Chile
Mr Locuace100 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

ld snp • 525 views
ADD COMMENTlink written 18 months ago by Mr Locuace100
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