LD pruning before or after phasing for calculating site frequency spectrum?
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5.8 years ago
Mr Locuace ▴ 180

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

SNP LD • 1.3k views
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