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.