Closed silvewheat closed 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.
Thanks for your answer.
Best wishes.
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%) ?