search

simonhmartin / tutorials

Tutorials on evolutionary genomics
41 stars 22 forks source link

How to calculate the proportion of introgression? #1

Closed silvewheat closed 4 years ago

silvewheat commented 5 years ago

Hello, After calculated the fd using sliding windows, how we calculate the proportion of introgressed regions arcoss the whole genomes? That is, how we determine the threshold of a introgressed window? Using top 5% and reduced dxy (also bottom 5%) ?

simonhmartin commented 4 years ago

Hello, I'm very sorry to have missed this question, now over a year ago!

My recommendation is not to use the fd value for windows to compute the genome-wide proportion of introgression. Instead, it would be better to compute a single genome-wide f estimate. There are tools such as Dsuite that can do that. Otherwise, my other tutorial shows a way to do it manually from allele frequency data.

silvewheat commented 4 years ago

Thanks for your answer.

Best wishes.