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.