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VAT mendelian commands - Revision history
2026-04-05T21:51:18Z
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Zhihuiz: Created page with "__NOTITLE__ ==VAT Menderlian == <pre> vtools -h vtools init VATDemo vtools import *.vcf.gz --var_info DP filter --geno_info DP_geno --build hg18 -j1 vtools liftover hg19 --fl..."
2018-06-13T17:40:49Z
<p>Created page with "__NOTITLE__ ==VAT Menderlian == <pre> vtools -h vtools init VATDemo vtools import *.vcf.gz --var_info DP filter --geno_info DP_geno --build hg18 -j1 vtools liftover hg19 --fl..."</p>
<p><b>New page</b></p><div>__NOTITLE__<br />
<br />
==VAT Menderlian ==<br />
<pre><br />
vtools -h<br />
vtools init VATDemo<br />
vtools import *.vcf.gz --var_info DP filter --geno_info DP_geno --build hg18 -j1<br />
vtools liftover hg19 --flip<br />
head phenotypes.csv<br />
vtools phenotype --from_file phenotypes.csv --delimiter ","<br />
vtools show project<br />
vtools show tables<br />
vtools show table variant<br />
vtools show samples<br />
vtools show genotypes<br />
vtools show fields<br />
vtools select variant --count<br />
vtools show genotypes > GenotypeSummary.txt<br />
head GenotypeSummary.txt<br />
vtools output variant "max(DP)" "min(DP)" "avg(DP)" "stdev(DP)" "lower_quartile(DP)" "upper_quartile(DP)" --header<br />
vtools select variant "filter='PASS'" --count<br />
vtools select variant "filter='PASS'" -o "max(DP)" "min(DP)" "avg(DP)" "stdev(DP)" "lower_quartile(DP)" "upper_quartile(DP)" --header<br />
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()'<br />
vtools show fields<br />
vtools show table variant<br />
vtools update variant --from_stat 'totalGD10=#(GT)' 'numGD10=#(alt)' 'hetGD10=#(het)' 'homGD10=#(hom)' 'otherGD10=#(other)' 'mafGD10=maf()' --genotypes "DP_geno > 10"<br />
vtools show fields <br />
vtools show table variant<br />
vtools output variant chr pos maf mafGD10 --header --limit 10<br />
vtools execute ANNOVAR geneanno<br />
vtools output variant chr pos ref alt mut_type --limit 10 --header<br />
vtools select variant "DP<15" -t to_remove<br />
vtools show tables<br />
vtools remove variants to_remove -v0<br />
vtools show tables<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 use ExAC.DB<br />
vtools show annotation ExAC<br />
vtools select v_funct "NFE_MAF<0.01" -t rare<br />
vtools use refGene<br />
vtools show annotation refGene<br />
vtools associate -h<br />
vtools show tests<br />
vtools show test LogitRegBurden<br />
vtools associate rare MD --covariate SEX -m "LogitRegBurden --alternative 2" -g refGene.name2 -j1 --to_db RV > RV_BRV.asso.res<br />
grep -i error *.log | tail -3<br />
less RV_BRV.asso.res<br />
sort -g -k6 RV_BRV.asso.res | head<br />
vtools associate rare MD --covariate SEX -m "VariableThresholdsBt --alternative 2 -p 100000 --adaptive 0.0005" -g refGene.name2 -j1 --to_db RV > RV_VT.asso.res<br />
grep -i error *.log | tail -5<br />
less RV_VT.asso.res<br />
sort -g -k6 RV_VT.asso.res | head<br />
vtools select rare "refGene.name2='SF3A2'" -o chr pos ref alt mafGD10 numGD10 mut_type --header<br />
vtools_report plot_association qq -o QQRV -b --label_top 2 -f 6 < RV_BRV.asso.res<br />
vtools_report plot_association manhattan -o MHRV -b --label_top 5 --color Dark2 --chrom_prefix None -f 6 < RV_BRV.asso.res<br />
</pre></div>
Zhihuiz