Question: LD pruning before or after phasing for calculating site frequency spectrum?
gravatar for Mr Locuace
2.4 years ago by
Mr Locuace100
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 • 734 views
ADD COMMENTlink written 2.4 years ago by Mr Locuace100
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: 1486 users visited in the last hour