recombination - christianparobek/cambodiaWGS GitHub Wiki

Also, see my page on gubbins work. And my page for LDhat.

Estimating Recombination:

LD and Recombo are related. May be possible to estimate recombination from popgen data like what we have. Here is a review: http://www.nature.com/nrg/journal/v4/n12/full/nrg1227.html Here is a paper in microbes: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245952/

We can use non-parametric (model-free) approaches to estimate the recombination rate in a population. However, these "greatly underestimate the true level of recombination that has occurred" (reviewed in Stumpf 2003). However, non-parametric approaches can be useful for detecting recombination hotspots.

The general equation for population recombination rate is:

rho = 4 Ne*r
where rho is the population recomb rate, Ne is the effective population size, and r is the per-generation recomb rate