Question: Can I estimate LD among species using SNP data?
gravatar for tianying
3.7 years ago by
tianying10 wrote:

I'm working on a project using SNP data from 9 closely related plant species. For each species, I only have one individual. All species were mapped to the same reference genome. I'm planning to do some phylogenetic and admixture analyses next, and I'm not sure if I should estimate the linkage disequilibrium among species? Any thoughts is appreciated!

snp sequence • 879 views
ADD COMMENTlink modified 3.7 years ago by Bioaln340 • written 3.7 years ago by tianying10
gravatar for Bioaln
3.7 years ago by
Bioaln340 wrote:

Conducting LD tests having only one individual might provide valuable insights into data, but be very careful, from my experience one individual on species level cannot clearly reveal all the differences present which might interest the researcher.

ADD COMMENTlink written 3.7 years ago by Bioaln340

I just want to use LD analysis to estimate the spacing filtering parameter. I actually ran a plink LD analysis. The result showed a dramatic decay after 20bp, and became stable after 50bp. So is it reasonable to use 50 bp spacing to filter my vcf file? Or is there any other method I can estimate the spacing parameter? Thanks!

ADD REPLYlink written 3.7 years ago by tianying10
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: 967 users visited in the last hour