vt1

Toolset for short variant discovery in genetic sequence data

Usage

vt <tool> [options]

`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

4 releases since Debian 1.3 (Bo); the text changed 1 time.