Using a within population reference genome - Recombination
How important is it that the reference genome is within- population or within- species of the recombination landscape you are trying to estimate or for variant calling in general?
I am calling variants to estimate recombination landscape using the program ReLERNN. My reference is of the same species, but I was wondering if I could also build one for distantly related species (~15 million years diverged) using the same reference?
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