vtools show fields
vtools show table variant
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 > 10"
vtools show fields
vtools show table variant
vtools output variant chr pos maf mafGD10 --header --limit 20
vtools phenotype --set "RACE=0" --samples "filename like ’YRI'YRI%’'" vtools phenotype --set "RACE=1" --samples "filename like ’CEU'CEU%’'"
vtools show samples --limit 10
vtools update variant --from_stat ’CEU_mafGD10'CEU_mafGD10=maf()’ ' --genotypes ’DP_geno'DP_geno>10’ 10' --samples "RACE=1" vtools update variant --from_stat ’YRI_mafGD10'YRI_mafGD10=maf()’ ' --genotypes ’DP_geno'DP_geno>10’ 10' --samples "RACE=0"
vtools output variant chr pos mafGD10 CEU_mafGD10 YRI_mafGD10 --header --limit 10
vtools phenotype --from_stat ’CEU_totalGD10'CEU_totalGD10=#(GT)’ ’CEU_numGD10' 'CEU_numGD10=#(alt)’ ' --genotypes ’DP_geno'DP_geno>10’ 10' --samples "RACE=1" vtools phenotype --from_stat ’YRI_totalGD10'YRI_totalGD10=#(GT)’ ’YRI_numGD10' 'YRI_numGD10=#(alt)’ ' --genotypes ’DP_geno'DP_geno>10’ 10' --samples "RACE=0"
vtools phenotype --output sample_nameCEU_totalGD10CEU_numGD10YRI_totalGD10YRI_numGD10 --header
vtools execute ANNOVAR geneanno
vtools show tables
vtools remove genotypes "DP_geno<10" -v0
vtools select variant "mut_type like ’non'non%’ ' or mut_type like ’stop'stop%’ ' or region_type=’splicing’'splicing'" -t v_funct
vtools show tables
vtools show samples --limit 5
less EA_RV_VT.asso.res
sort -g -k6 EA_RV_VT.asso.res | head
vtools select rare_ceu "refGene.name2=’ABCC1’'ABCC1'" -o chr pos ref alt CEU_mafGD10 numGD10 mut_type --header
cd ..
vtools select variant --samples "RACE=0" -t YRI