==VAT==
ulimit -s 8000
vtools -h
vtools select rare_ceu "refGene.name2='ABCC1'" -o chr pos ref alt CEU_mafGD10 numGD10 mut_type --header
vtools_report plot_association qq -o QQRV -b --label_top 2 -f 6 < EA_RV.asso.res
vtools_report plot_association manhattan -o MHRV -b --label_top 5 --color Dark2 --chrom_prefix None -f 6 < EA_RV.asso.res <br />vtools associate rare_ceu BMI --covariate SEX KING_MDS1 KING_MDS2 -m "LinRegBurden --name RVMDS2 --alternative 2" -g refGene.name2 -j1 --to_db EA_RV > EA_RV_MDS2.asso.res
vtools_report plot_association qq -o QQRV_MDS2 -b --label_top 2 -f 6 < EA_RV_MDS2.asso.res <br />cd .. <br />vtools select variant --samples "RACE=0" -t YRI <br />mkdir -p yri <br />cd yri <br />vtools init yri --parent ../ --variants YRI --samples "RACE=0" --build hg19 <br />vtools select variant "YRI_mafGD10>=0.05" -t common_yri
vtools select v_funct "YRI_mafGD10<0.01" -t rare_yri <br />vtools use refGene <br />vtools associate common_yri BMI --covariate SEX -m "LinRegBurden --alternative 2" -j1 --to_db YA_CV > YA_CV.asso.res