View source for VAT mendelian commands

__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 --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 10
vtools execute ANNOVAR geneanno
vtools output variant chr pos ref alt mut_type --limit 10 --header
vtools select variant "DP<15" -t to_remove
vtools show tables
vtools remove variants to_remove -v0
vtools show tables
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 use ExAC.DB
vtools show annotation ExAC
vtools select v_funct "NFE_MAF<0.01" -t rare
vtools use refGene
vtools show annotation refGene
vtools associate -h
vtools show tests
vtools show test LogitRegBurden
vtools associate rare MD --covariate SEX -m "LogitRegBurden --alternative 2" -g refGene.name2 -j1 --to_db RV > RV_BRV.asso.res
grep -i error *.log | tail -3
less RV_BRV.asso.res
sort -g -k6 RV_BRV.asso.res | head
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
grep -i error *.log | tail -5
less RV_VT.asso.res
sort -g -k6 RV_VT.asso.res | head
vtools select rare "refGene.name2='SF3A2'" -o chr pos ref alt mafGD10 numGD10 mut_type --header
vtools_report plot_association qq -o QQRV -b --label_top 2 -f 6 < RV_BRV.asso.res
vtools_report plot_association manhattan -o MHRV -b --label_top 5 --color Dark2 --chrom_prefix None -f 6 < RV_BRV.asso.res
</pre>