Changes

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

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

grep -i error *.log | tail -2210

grep -i error *.log | tail -2210

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

vtools select v_funct "YRI_mafGD10<0.01" -t rare_yri <br />vtools use refGene vtools associate common_yri BMI --covariate SEX -m "LinRegBurden --alternative 2" -j1 --to_db YA_CV > YA_CV.asso.res

cut -f1,3 META_RV_VT.asso.res | head==VMT==  ################################## # Example 1: Autosomal recessive # ################################## vtools init VMT --force vtools import AR1.vcf.gz AR2.vcf.gz --format NSHI.fmt --build hg19 -j8 vtools show tables vtools show samples vtools execute ANNOVAR geneanno vtools use dbNSFP.DB vtools use refGene vtools show fields vtools select variant "(ExAC_AF is NULL or ExAC_AF<0.0005) AND (ExAC_SAS_AF is NULL or ExAC_SAS_AF<0.0005)" -t ExAC0005 vtools select ExAC0005 "CADD_phred>20 or CADD_phred is NULL" -t CADD20 vtools select CADD20 "region_type is 'splicing' OR (mut_type is not NULL AND mut_type is not 'synonymous SNV' AND mut_type is not 'unknown')" -t ANNOVARtype vtools select ANNOVARtype "dbNSFP.chr is not null" --output chr pos ref alt sift_pred lrt_pred fathmm_pred mutationtaster_pred mutationassessor_pred polyphen2_hdiv_pred polyphen2_hvar_pred provean_pred MetaLR_pred MetaSVM_pred >snv.txt python choose_damaging_variants.py snv.txt vtools update ANNOVARtype --format VMT_annotation.fmt --from_file snv.txt.parsed vtools select ANNOVARtype "vmt_annotation='damaging_SNV'" -t damaging vtools select damaging "chr=16 AND (pos>=63600000 AND pos<=79700000)" -o chr pos ref alt region_type region_name mut_type function rs_dbSNP141 ExAC_Adj_AF ExAC_SAS_AF CADD_phred FATHMM_pred LRT_pred MetaLR_pred MetaSVM_pred MutationAssessor_pred MutationTaster_pred Polyphen2_HDIV_pred Polyphen2_HVAR_pred PROVEAN_pred SIFT_pred "samples('geno_filter=GT=1')" "samples('geno_filter=GT=2')" vtools update damaging --from_stat "totX=#(GT)" "homX=#(hom)" --samples "sample_name='L1' OR sample_name='L2'" -j2 vtools select damaging "totX=homX AND totX=2" -t homL1_L2 vtools remove fields totX homX vtools output homL1_L2 chr pos ref alt region_type region_name mut_type function rs_dbSNP141 ExAC_Adj_AF ExAC_SAS_AF CADD_phred FATHMM_pred LRT_pred MetaLR_pred MetaSVM_pred MutationAssessor_pred MutationTaster_pred Polyphen2_HDIV_pred Polyphen2_HVAR_pred PROVEAN_pred SIFT_pred "samples('geno_filter=GT=1')" "samples('geno_filter=GT=2')" ################################## # Example 2: Autosomal dominant # ################################## vtools import AD.vcf.gz --format NSHI.fmt --build hg19 -j8 vtools show tables vtools show samples vtools select variant "(ExAC_AF is NULL or ExAC_AF<0.0005) AND (ExAC_NFE_AF is NULL or ExAC_NFE_AF<0.0005)" --samples "sample_name='AD1' OR sample_name='AD2'" -t ExAC0005_AD vtools select ExAC0005_AD "CADD_phred>15 or CADD_phred is NULL" -t CADD15_AD vtools select CADD15_AD "dbNSFP.chr is not null" --output chr pos ref alt sift_pred lrt_pred fathmm_pred mutationtaster_pred mutationassessor_pred polyphen2_hdiv_pred polyphen2_hvar_pred provean_pred MetaLR_pred MetaSVM_pred >snv.txt python choose_damaging_variants.py snv.txt vtools update variant --format VMT_annotation.fmt --from_file snv.txt.parsed vtools select CADD15_AD "vmt_annotation='damaging_SNV'" -t damaging_AD vtools update damaging_AD --from_stat "totX=#(GT)" "hetX=#(het)" --samples "sample_name='AD1' OR sample_name='AD2'" -j2 vtools select damaging_AD "totX=hetX AND totX=2" -t hetAD_2 vtools remove fields totX hetX vtools output hetAD_2 chr pos ref alt refGene.name2 rs_dbSNP141 ExAC_Adj_AF ExAC_SAS_AF CADD_phred FATHMM_pred LRT_pred MetaLR_pred MetaSVM_pred MutationAssessor_pred MutationTaster_pred Polyphen2_HDIV_pred Polyphen2_HVAR_pred PROVEAN_pred SIFT_pred "samples('geno_filter=GT=1')" "samples('geno_filter=GT=2')" ################################## # Example 3: De Novo # ################################## vtools import de_novo.vcf.gz --format NSHI.fmt --build hg19 -j8 vtools show tables vtools show samples vtools update variant --from_stat "totX=#(GT)" "hetX=#(het)" --samples "sample_name='Son'" -j2 vtools select variant "totX=hetX AND totX=1" -t Son_het vtools update Son_het --from_stat "totX=#(GT)" "wtX=#(wtGT)" --samples "sample_name='Dad' OR sample_name='Mom'" -j2 vtools select Son_het "(totX=wtX AND totX=2) and ((ExAC_AF is NULL or ExAC_AF<0.0005) AND (ExAC_NFE_AF is NULL or ExAC_NFE_AF<0.0005))" -t deNovo vtools output deNovo chr pos ref alt refGene.name2 rs_dbSNP141 ExAC_Adj_AF ExAC_NFE_AF CADD_phred FATHMM_pred LRT_pred MetaLR_pred MetaSVM_pred MutationAssessor_pred MutationTaster_pred Polyphen2_HDIV_pred Polyphen2_HVAR_pred PROVEAN_pred SIFT_pred "samples('geno_filter=GT=1')" "samples('geno_filter=GT=2')"