Difference between revisions of "VAT Exercise"

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(Created page with "__NOTITLE__ ==VAT== vtools -h vtools init VATDemo vtools import *.vcf.gz --var_info DP filter --geno_info DP_geno --build hg18 -j1 vtools liftover hg19 head phenotypes.cs...")
 
 
(2 intermediate revisions by the same user not shown)
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__NOTITLE__
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__NOTITLE__==VAT==
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==VAT==
+
 
 
  vtools -h
 
  vtools -h
 
  vtools init VATDemo
 
  vtools init VATDemo
 
  vtools import *.vcf.gz --var_info DP filter --geno_info DP_geno --build hg18 -j1
 
  vtools import *.vcf.gz --var_info DP filter --geno_info DP_geno --build hg18 -j1
−
  vtools liftover hg19
+
  vtools liftover hg19 --flip
 
  head phenotypes.csv
 
  head phenotypes.csv
 
  vtools phenotype --from_file phenotypes.csv --delimiter ","
 
  vtools phenotype --from_file phenotypes.csv --delimiter ","
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  vtools phenotype --from_stat 'YRI_totalGD10=#(GT)' 'YRI_numGD10=#(alt)' --genotypes 'DP_geno>10' --samples "RACE=0"
 
  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 phenotype --output sample_name CEU_totalGD10 CEU_numGD10 YRI_totalGD10 YRI_numGD10 --header
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vtools select variant 'maf>=0.01' -t variant_MAFge01 'Variants that have MAF >= 0.01'
 
−
vtools show tables
 
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vtools execute KING --var_table variant_MAFge01
 
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vtools_report plot_pheno_fields KING_MDS1 KING_MDS2 RACE --dot KING.mds.race.pdf --discrete_color Dark2
 
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vtools_report plot_pheno_fields KING_MDS1 KING_MDS2 panel --dot KING.mds.panel.pdf --discrete_color Dark2
 
 
  vtools execute ANNOVAR geneanno
 
  vtools execute ANNOVAR geneanno
 
  vtools output variant chr pos ref alt mut_type --limit 20 --header
 
  vtools output variant chr pos ref alt mut_type --limit 20 --header
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  vtools remove variants to_remove -v0
 
  vtools remove variants to_remove -v0
 
  vtools show tables
 
  vtools show tables
−
  vtools remove genotypes "DP_geno&lt;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 remove genotypes "DP_geno&lt;10" -v0   
 +
vtools select variant "mut_type like 'non%' or mut_type like 'stop%' or region_type='splicing'" -t v_funct   
 +
vtools show tables   
 +
vtools show samples --limit 5   
 +
vtools select variant --samples "RACE=1" -t CEU   
 +
mkdir -p ceu  
 +
cd ceu  
 +
vtools init ceu --parent ../ --variants CEU --samples "RACE=1" --build hg19
 
  vtools show project
 
  vtools show project
 
  vtools select variant "CEU_mafGD10&gt;=0.05" -t common_ceu
 
  vtools select variant "CEU_mafGD10&gt;=0.05" -t common_ceu
−
  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 select v_funct "CEU_mafGD10&lt;0.01" -t rare_ceu   
 +
vtools use refGene   
 +
vtools show annotation refGene  
 +
  vtools associate -h   
 +
vtools show tests   
 +
vtools show test LinRegBurden  
 +
vtools associate common_ceu BMI --covariate SEX -m "LinRegBurden --alternative 2" -j1 --to_db EA_CV &gt; EA_CV.asso.res
 
  grep -i error *.log
 
  grep -i error *.log
 
  less EA_CV.asso.res
 
  less EA_CV.asso.res
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  vtools show fields
 
  vtools show fields
 
  vtools associate rare_ceu BMI --covariate SEX -m "LinRegBurden --alternative 2" -g refGene.name2 -j1 --to_db EA_RV &gt; EA_RV.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 -22
+
  grep -i error *.log | tail -10
 
  less EA_RV.asso.res
 
  less EA_RV.asso.res
 
  sort -g -k6 EA_RV.asso.res | head
 
  sort -g -k6 EA_RV.asso.res | head
 
  vtools associate rare_ceu BMI --covariate SEX -m "VariableThresholdsQt --alternative 2 -p 100000 --adaptive 0.0005" -g refGene.name2 -j1 --to_db EA_RV &gt; EA_RV_VT.asso.res
 
  vtools associate rare_ceu BMI --covariate SEX -m "VariableThresholdsQt --alternative 2 -p 100000 --adaptive 0.0005" -g refGene.name2 -j1 --to_db EA_RV &gt; EA_RV_VT.asso.res
−
  grep -i error *.log | tail -22
+
  grep -i error *.log | tail -10
 
  less EA_RV_VT.asso.res
 
  less EA_RV_VT.asso.res
 
  sort -g -k6 EA_RV_VT.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 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 &lt; EA_RV.asso.res
+
  cd ..   
−
  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 select variant --samples "RACE=0" -t YRI  
−
  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
+
mkdir -p 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
+
cd yri  
 +
vtools init yri --parent ../ --variants YRI --samples "RACE=0" --build hg19  
 +
vtools select variant "YRI_mafGD10&gt;=0.05" -t common_yri
 +
  vtools select v_funct "YRI_mafGD10&lt;0.01" -t rare_yri   
 +
vtools use refGene   
 +
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 "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 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

Latest revision as of 17:52, 24 January 2019

==VAT== 

vtools -h
vtools init VATDemo
vtools import *.vcf.gz --var_info DP filter --geno_info DP_geno --build hg18 -j1
vtools liftover hg19 --flip
head phenotypes.csv
vtools phenotype --from_file phenotypes.csv --delimiter ","
vtools show project
vtools show tables
vtools show table variant
vtools show samples
vtools show genotypes
vtools show fields
vtools select variant --count
vtools show genotypes > GenotypeSummary.txt
head GenotypeSummary.txt
vtools output variant "max(DP)" "min(DP)" "avg(DP)" "stdev(DP)" "lower_quartile(DP)" "upper_quartile(DP)" --header
vtools select variant "filter='PASS'" --count
vtools select variant "filter='PASS'" -o "max(DP)" "min(DP)" "avg(DP)" "stdev(DP)" "lower_quartile(DP)" "upper_quartile(DP)" --header
vtools update variant --from_stat 'total=#(GT)' 'num=#(alt)' 'het=#(het)' 'hom=#(hom)' 'other=#(other)' 'minDP=min(DP_geno)' 'maxDP=max(DP_geno)' 'meanDP=avg(DP_geno)' 'maf=maf()'
vtools show fields
vtools show table variant
vtools update variant --from_stat 'totalGD10=#(GT)' 'numGD10=#(alt)' 'hetGD10=#(het)' 'homGD10=#(hom)' 'otherGD10=#(other)' '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%'"
vtools phenotype --set "RACE=1" --samples "filename like 'CEU%'"
vtools show samples --limit 10
vtools update variant --from_stat 'CEU_mafGD10=maf()' --genotypes 'DP_geno>10' --samples "RACE=1"
vtools update variant --from_stat 'YRI_mafGD10=maf()' --genotypes 'DP_geno>10' --samples "RACE=0"
vtools output variant chr pos mafGD10 CEU_mafGD10 YRI_mafGD10 --header --limit 10
vtools phenotype --from_stat 'CEU_totalGD10=#(GT)' 'CEU_numGD10=#(alt)' --genotypes 'DP_geno>10' --samples "RACE=1"
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 execute ANNOVAR geneanno
vtools output variant chr pos ref alt mut_type --limit 20 --header
vtools_report trans_ratio variant -n num
vtools_report trans_ratio variant -n numGD10
vtools select variant "DP<15" -t to_remove
vtools show tables
vtools remove variants to_remove -v0
vtools show tables
vtools remove genotypes "DP_geno<10" -v0  
vtools select variant "mut_type like 'non%' or mut_type like 'stop%' or region_type='splicing'" -t v_funct  
vtools show tables  
vtools show samples --limit 5  
vtools select variant --samples "RACE=1" -t CEU  
mkdir -p ceu 
cd ceu 
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  
vtools use refGene  
vtools show annotation refGene 
vtools associate -h  
vtools show tests  
vtools show test LinRegBurden 
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
sort -g -k7 EA_CV.asso.res | head
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 -10
less EA_RV.asso.res
sort -g -k6 EA_RV.asso.res | head
vtools associate rare_ceu BMI --covariate SEX -m "VariableThresholdsQt --alternative 2 -p 100000 --adaptive 0.0005" -g refGene.name2 -j1 --to_db EA_RV > EA_RV_VT.asso.res
grep -i error *.log | tail -10
less EA_RV_VT.asso.res
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
cd ..  
vtools select variant --samples "RACE=0" -t YRI 
mkdir -p yri 
cd yri 
vtools init yri --parent ../ --variants YRI --samples "RACE=0" --build hg19 
vtools select variant "YRI_mafGD10>=0.05" -t common_yri
vtools select v_funct "YRI_mafGD10<0.01" -t rare_yri  
vtools use refGene  
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
cd ..
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 > META_RV_VT.asso.res
cut -f1,3 META_RV_VT.asso.res | head
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