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View Full Version : How to get a bayenv2 usable file from a .geno file



Nuthatch
07-24-2020, 08:37 AM
I have a .geno file (https://reichdata.hms.harvard.edu/pub/datasets/amh_repo/curated_releases/V42/V42.4/SHARE/public.dir/v42.4.1240K_HO.geno), containing genotypes of present-day and ancient individuals (https://reich.hms.harvard.edu/downloadable-genotypes-present-day-and-ancient-dna-data-compiled-published-papers). What I want to do is to use bayenv2 on these data, looking for a correlation between alleles frequencies and a specific environmental variable. In particular, I'm interested only in modern individuals, that is the individuals with "present" in the 7th column of the .anno file (https://reichdata.hms.harvard.edu/pub/datasets/amh_repo/curated_releases/V42/V42.4/SHARE/public.dir/v42.4.1240K_HO.anno). So, what I'd like to know is what I need to do with the initial .geno file in order to obtain a file that is bayenv2 usable and that contains only the genetic information about modern individuals. Thank you.