vtools phenotype --from_stat 'YRI_totalGD10=#(GT)' 'YRI_numGD10=#(alt)' --genotypes 'DP_geno>10' --samples "RACE=0"
vtools phenotype --output sample_name CEU_totalGD10 CEU_numGD10 YRI_totalGD10 YRI_numGD10 --header
vtools select variant 'maf>=0.01' -t variant_MAFge01 'Variants that have MAF >= 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 execute ANNOVAR geneanno
vtools output variant chr pos ref alt mut_type --limit 20 --header
vtools remove variants to_remove -v0
vtools show tables
vtools remove genotypes "DP_geno<10" -v0 <br /> vtools select variant "mut_type like 'non%' or mut_type like 'stop%' or region_type='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 variant "CEU_mafGD10>=0.05" -t common_ceu
vtools select v_funct "CEU_mafGD10<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 > EA_CV.asso.res
grep -i error *.log
less EA_CV.asso.res
vtools show fields
vtools associate rare_ceu BMI --covariate SEX -m "LinRegBurden --alternative 2" -g refGene.name2 -j1 --to_db EA_RV > EA_RV.asso.res
grep -i error *.log | tail -2210
less EA_RV.asso.res
sort -g -k6 EA_RV.asso.res | head
sort -g -k6 EA_RV_VT.asso.res | head
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_RVcd .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
vtools associate rare_yri BMI --covariate SEX -m "LinRegBurden --alternative 2" -g refGene.name2 -j1 --to_db YA_RV > 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 > YA_RV_VT.asso.res