Preparing HapMap dataset for tutorial

Download 1KGP data

Download HapMap.

cd ~/gwas_exercises/

mkdir prep_hapmap

cd prep_hapmap

wget https://ftp.ncbi.nlm.nih.gov/hapmap/genotypes/hapmap3_r3/plink_format/hapmap3_r3_b36_fwd.consensus.qc.poly.map.gz

wget https://ftp.ncbi.nlm.nih.gov/hapmap/genotypes/hapmap3_r3/plink_format/hapmap3_r3_b36_fwd.consensus.qc.poly.ped.gz

gzip -d *gz

wget https://ftp.ncbi.nlm.nih.gov/hapmap/genotypes/hapmap3_r3/relationships_w_pops_041510.txt

Make binary plink files.

plink --file hapmap3_r3_b36_fwd.consensus.qc.poly --make-bed --out hapmap3_r3

Adding outlier individuals to European individuals

Make list of (randomply chosen) FID individuals to keep as outliers.

echo "Y057" > keep_outliers_FID
echo "Y058" >> keep_outliers_FID
echo "Y059" >> keep_outliers_FID

Extract outlier individuals from original HapMap dataset.

plink --bfile hapmap3_r3 --keep <(grep -f keep_outliers_FID hapmap3_r3.fam) --make-bed --out keep_outliers

Merge outlier individuals with European HapMap data (from Marees 2018 tutorial - this file is not presenti in repository) and save them in data directory.

plink --bfile HapMap_3_r3_1 --bmerge keep_outliers --make-bed --out hapmap