# you should have gcta64 in your current directory, and a folder `Data/PartF/' where the data is stored.


### RUN on your own time, outside with practical
./gcta64 --bfile Data/PartF/optional/QIMRX_cleaned --make-grm --autosome --out Results/QIMRX --thread-num 2
./gcta64 --grm Results/QIMRX --grm-cutoff 0.8 --make-grm --out Data/PartF/QIMRX_no_twin

./gcta64  --bfile Data/PartF/optional/QIMRX_cleaned_small --make-grm --autosome \
          --out Results/QIMRX_small
####


# estimating variance components for height (phenotype 1) and serum transferrin (phenotype 2).
./gcta64  --grm Data/PartF/QIMRX_no_twin  --pheno Data/PartF/HT_T_X.pheno --mpheno 1 \
          --reml --out Results/QIMRX_1
./gcta64  --grm data/PartF/QIMRX_no_twin  --pheno data/PartF/HT_T_X.pheno --mpheno 2 \
          --reml --out Results/QIMRX_2


#-----------------#
###  Exercise   ###
#-----------------#

# removing relatives
./gcta64 --grm Data/PartF/QIMRX_no_twin  --grm-cutoff 0.05 --make-grm --out Results/QIMRX_nr

# estimating variance components for height (phenotype 1) and serum transferrin (phenotype 2) without relatives
./gcta64 --grm Results/QIMRX_nr --pheno Data/PartF/HT_T_X.pheno --mpheno 1 --reml --out Results/QIMRX_1_nr
./gcta64 --grm Results/QIMRX_nr --pheno Data/PartF/HT_T_X.pheno --mpheno 2 --reml --out Results/QIMRX_2_nr


#-----------------#
###  Exercise   ###
#-----------------#

### RUN on your own time, outside with practical
./gcta64  --bfile Data/PartF/optional/QIMRX_cleaned --extract Data/PartF/bot_maf_snps.txt --autosome \
          --make-grm  --keep  Results/QIMRX_nr.grm.id --thread-num 2 --out Data/PartF/QIMRX_nr_bot_maf_snps
./gcta64  --bfile Data/PartF/optional/QIMRX_cleaned --extract Data/PartF/top_maf_snps.txt --autosome \
          --make-grm  --keep Results/QIMRX_nr.grm.id --thread-num 2 --out Data/PartF/QIMRX_nr_top_maf_snps
####



# partitioning by MAF
./gcta64  --mgrm Data/PartF/QIMRX_multi.txt --pheno Data/PartF/HT_T_X.pheno --mpheno 1 --reml --out Results/QIMRX_1_multi_nr 
./gcta64  --mgrm Data/PartF/QIMRX_multi.txt --pheno Data/PartF/HT_T_X.pheno --mpheno 2 --reml --out Results/QIMRX_1_multi_nr