#all bash commands

cd igss

#this creates binaries from the original hapmap files which were raw text
##plink --file ./hapmap3_pop/hapmap3_r2_b36_fwd.CEU.qc.poly --make-bed --out ceu  #time consuming, i ran for you.

#this prunes the ceu files. three filters were imposed: genotype missingness, maf, and hwe
plink --bfile ceu  --geno 0.05  --maf .01 --hwe 0.001 --make-bed --out ceu-qc 

#smaller set of markers just to make our lives easier.
plink --bfile ceu-qc  --thin 0.3 --make-bed --out ceu-qc-small --seed 1444792558






#prune for LD: not needed for tutorial
#./plink --bfile ceu-qc --indep-pairwise 50 5 0.2 --out ceu-le #this identifies those makers in ld & le 
#./plink --bfile ceu-qc --extract ceu-le.prune.in --make-bed --out ceu-le #this pulls out the LE set of markers from the previous step.