vt - toolset for short variant discovery in genetic sequence data

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

vt 0.57721+ds                                       June 2020                                              VT(1)

       vt - toolset for short variant discovery in genetic sequence data

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

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