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TIPS
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- download the data: e.g. wget
- uncompress the data (tar.gz file: e.g. gunzip, tar)
- look at the data: phenotypes? genotypes?
- the genotypes are in the Plink binary format!
- you’ll need the –bfile option to read them with Plink
- you can check the Plink online manual: https://www.cog-genomics.org/plink/
- (it’s always a good thing to learn to use the internet to look for code syntax help)
- subset the genotype files (and maybe convert to ped/map)
- anything to be done with the phenotypes?
- you can make more than one script for data preprocessing: e.g. 
        i) script to download the data; 
        ii) script to prepare the genotype data (e.g. using Plink); 
        iii) Rscript to prepare the phenotype data (but you can use bash or something else if you prefer)
- then continue with data filtering (MAF, call-rate etc.), imputation of missing genotypes and the GWAS model