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.