==VAT Commands in Exercise==
<pre> vtools -h
vtools init VATDemo
vtools import *.vcf.gz --var_info DP filter --geno_info DP_geno --build hg18 -j1
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’'PASS'" --count vtools select variant "filter=’PASS’'PASS'" -o "max(DP)" "min(DP)" "avg(DP)" "stdev(DP)" "lower_quartile(DP)" "upper_quartile(DP)" --header vtools update variant --from_stat ’total'total=#(GT)’ ’num' 'num=#(alt)’ ’het' 'het=#(het)’ ’hom' 'hom=#(hom)’ ’other' 'other=#(other)’ ’minDP' 'minDP=min(DP_geno)’ ’maxDP' 'maxDP=max(DP_geno)’ ’meanDP' 'meanDP=avg(DP_geno)’ ’maf' 'maf=maf()’'
vtools show fields
vtools show table variant