VT(1)

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.