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PalamaraLab / HapNe

Haplotype-based inference of recent effective population size in modern and ancient DNA samples
GNU General Public License v3.0
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Problem with genetic map #2

Open GrazieT opened 1 month ago

GrazieT commented 1 month ago

Hi, How can i get the genetic distance about genetic map from my vcf? I haven't the genetic map . Could you help me out? Much appreciate!

rmnfournier commented 1 month ago

Hi! Genetic maps can be downloaded from various sources, e.g. https://github.com/odelaneau/shapeit5/tree/main/resources/maps

GrazieT commented 1 month ago

Hi! Genetic maps can be downloaded from various sources, e.g. https://github.com/odelaneau/shapeit5/tree/main/resources/maps

Hi, thank you very much for your reply, but the species (plants) I studied have not found a known genetic map. Can I infer the recombination rate from my population vcf file before using HapNe? If possible, can you recommend a few software to calculate the recombination rate?