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

ld snp • 437 views
ADD COMMENTlink written 14 months ago by Mr Locuace90
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2089 users visited in the last hour