---
name: "vt"
section: "1"
platform: "linux"
package: "vt"
version: "0.57721+ds-3+b1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/vt"
---

# vt(1)

toolset for short variant discovery in genetic sequence data

## NAME

vt - toolset for short variant discovery in genetic sequence data

## SYNOPSIS

**vt** \<tool\> \[options\]

## TOOLS

- view

  view vcf/vcf.gz/bcf files

- index

  index vcf.gz/bcf files

- normalize

  normalize variants

- decompose

  decompose variants

- uniq

  drop duplicate variants

- cat

  concatenate VCF files

- paste

  paste VCF files

- sort

  sort VCF files

- subset

  subset VCF file to variants polymorphic in a sample

- peek

  summary of variants in the vcf file

- partition

  partition variants

- multi\_partition

  partition variants from multiple VCF files

- annotate\_variants

  annotate variants

- annotate\_db\_rsid

  annotate variants with dbSNP rsid

- annotate\_1000g

  annotate variants with 1000 Genomes variants

- annotate\_regions

  annotate regions

- compute\_concordance

  compute genotype concordance between 2 call sets

- compute\_features

  compute genotype likelihood based statistics

- discover

  discover variants

- genotype

  genotype variants

## SEE ALSO

Help page on http://statgen.sph.umich.edu/wiki/Vt

## AUTHOR

 This manpage was written by Andreas Tille for the Debian distribution and\
  can be used for any other usage of the program.