Pre-processing PLINK files

Create a new directory called processed_data to store processed files

mkdir processed_data

Set minimum allele frequency (maf) to 0.05

plink --bfile original_data/grantsThomsons2017_maxMissing0.2 --maf 0.05 --no-sex --make-bed --out processed_data/grants_maf0.05

Change family ID to locality/species

Use given information from gazelle_popinfo_withPLINKid.txt to set the family IDs (1st column in .fam) to either locality or species.

plink --bfile processed_data/grants_maf0.05 --update-ids additional_files/locality_as_fam_ID.txt --make-bed -out processed_data/locality_grants

plink --bfile processed_data/grants_maf0.05 --update-ids additional_files/species_as_fam_ID.txt --make-bed -out processed_data/species_grants