Changes

 <pre> vtools -h

vtools select variant "filter='PASS'’PASS’" --count vtools select variant "filter='PASS'’PASS’" -o "max(DP)" "min(DP)" "avg(DP)" "stdev(DP)" "lower_quartile(DP)" "upper_quartile(DP)" --header vtools update variant --from_stat 'total’total=#(GT)' 'num’ ’num=#(alt)' 'het’ ’het=#(het)' 'hom’ ’hom=#(hom)' 'other’ ’other=#(other)' 'minDP’ ’minDP=min(DP_geno)' 'maxDP’ ’maxDP=max(DP_geno)' 'meanDP’ ’meanDP=avg(DP_geno)' 'maf’ ’maf=maf()'’

vtools update variant --from_stat 'totalGD10’totalGD10=#(GT)' 'numGD10’ ’numGD10=#(alt)' 'hetGD10’ ’hetGD10=#(het)' 'homGD10’ ’homGD10=#(hom)' 'otherGD10’ ’otherGD10=#(other)' 'mafGD10’ ’mafGD10=maf()' ’ --genotypes "DP_geno &gt; 10"

vtools phenotype --set "RACE=0" --samples "filename like 'YRI’YRI%'’" vtools phenotype --set "RACE=1" --samples "filename like 'CEU’CEU%'’"

vtools update variant --from_stat 'CEU_mafGD10’CEU_mafGD10=maf()' ’ --genotypes 'DP_geno’DP_geno&gt;10' 10’ --samples "RACE=1" vtools update variant --from_stat 'YRI_mafGD10’YRI_mafGD10=maf()' ’ --genotypes 'DP_geno’DP_geno&gt;10' 10’ --samples "RACE=0"

vtools phenotype --from_stat 'CEU_totalGD10’CEU_totalGD10=#(GT)' 'CEU_numGD10’ ’CEU_numGD10=#(alt)' ’ --genotypes 'DP_geno’DP_geno&gt;10' 10’ --samples "RACE=1" vtools phenotype --from_stat 'YRI_totalGD10’YRI_totalGD10=#(GT)' 'YRI_numGD10’ ’YRI_numGD10=#(alt)' ’ --genotypes 'DP_geno’DP_geno&gt;10' 10’ --samples "RACE=0" vtools phenotype --output sample_name CEU_totalGD10 CEU_numGD10 YRI_totalGD10 YRI_numGD10 sample_nameCEU_totalGD10CEU_numGD10YRI_totalGD10YRI_numGD10 --header vtools select variant 'maf&gt;=0.01' -t variant_MAFge01 'Variants that have MAF &gt;= 0.01' vtools show tables vtools execute KING --var_table variant_MAFge01 vtools_report plot_pheno_fields KING_MDS1 KING_MDS2 RACE --dot KING.mds.race.pdf --discrete_color Dark2 vtools_report plot_pheno_fields KING_MDS1 KING_MDS2 panel --dot KING.mds.panel.pdf --discrete_color Dark2

vtools remove genotypes "DP_geno&lt;10" -v0 <br />vtools select variant "mut_type like 'non’non%' ’ or mut_type like 'stop’stop%' ’ or region_type='splicing'’splicing’" -t v_funct <br />vtools show tables <br />vtools show samples --limit 5 <br />vtools select variant --samples "RACE=1" -t CEU <br />mkdir -p ceu <br /> cd ceu <br /> vtools init ceu --parent ../ --variants CEU --samples "RACE=1" --build hg19 vtools show project

vtools select v_funct "CEU_mafGD10&lt;0.01" -t rare_ceu <br />vtools use refGene <br />vtools show annotation refGene <br />vtools associate -h <br />vtools show tests <br />vtools show test LinRegBurden <br /> vtools associate common_ceu BMI --covariate SEX -m "LinRegBurden --alternative 2" -j1 --to_db EA_CV &gt; EA_CV.asso.res

vtools associate rare_ceu BMI --covariate SEX -m "LinRegBurden --alternative 2" -g refGene.name2 -j1 --to_db EA_RV &gt; EA_RV.asso.res grep -i error *.log | tail -2210

grep -i error *.log | tail -2210

vtools select rare_ceu "refGene.name2='ABCC1'’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 &lt; EA_RVcd .asso.res vtools_report plot_association manhattan -o MHRV -b --label_top 5 --color Dark2 --chrom_prefix None -f 6 &lt; 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 &gt; EA_RV_MDS2.asso.res vtools_report plot_association qq -o QQRV_MDS2 -b --label_top 2 -f 6 &lt; 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&gt;=0.05" -t common_yri vtools select v_funct "YRI_mafGD10&lt;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 &gt; YA_CV.asso.res vtools associate rare_yri BMI --covariate SEX -m "LinRegBurden --alternative 2" -g refGene.name2 -j1 --to_db YA_RV &gt; YA_RV.asso.res vtools associate rare_yri BMI --covariate SEX -m "VariableThresholdsQt --alternative 2 -p 100000 --adaptive 0.0005" -g refGene.name2 -j1 --to_db YA_RV &gt; YA_RV_VT.asso.res

vtools_report meta_analysis ceu/EA_RV_VT.asso.res yri/YA_RV_VT.asso.res --beta 5 --pval 6 --se 7 -n 2 --link 1 &gt; META_RV_VTME\ TA_RV_VT.asso.res