.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.15.
.TH VT "1" "June 2020" "vt 0.57721+ds" "User Commands"
.SH NAME
vt \- toolset for short variant discovery in genetic sequence data
.SH SYNOPSIS
.B vt
<tool> [options]
.SH TOOLS
.TP
view
view vcf/vcf.gz/bcf files
.TP
index
index vcf.gz/bcf files
.TP
normalize
normalize variants
.TP
decompose
decompose variants
.TP
uniq
drop duplicate variants
.TP
cat
concatenate VCF files
.TP
paste
paste VCF files
.TP
sort
sort VCF files
.TP
subset
subset VCF file to variants polymorphic in a sample
.TP
peek
summary of variants in the vcf file
.TP
partition
partition variants
.TP
multi_partition
partition variants from multiple VCF files
.TP
annotate_variants
annotate variants
.TP
annotate_db_rsid
annotate variants with dbSNP rsid
.TP
annotate_1000g
annotate variants with 1000 Genomes variants
.TP
annotate_regions
annotate regions
.TP
compute_concordance
compute genotype concordance between 2 call sets
.TP
compute_features
compute genotype likelihood based statistics
.TP
discover
discover variants
.TP
genotype
genotype variants
.SH SEE ALSO
Help page on http://statgen.sph.umich.edu/wiki/Vt
.SH AUTHOR
 This manpage was written by Andreas Tille for the Debian distribution and
 can be used for any other usage of the program.