.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.16.
.TH VG "1" "December 2020" "vg version v1.29.0 "Sospiro"" "User Commands"
.SH NAME
vg \- tools for working with genome variation graphs
.SH DESCRIPTION
vg: variation graph tool, version v1.29.0 "Sospiro"
.PP
usage: vg <command> [options]
.SS "main mapping and calling pipeline:"
.TP
\fB\-\-\fR construct
graph construction
.TP
\fB\-\-\fR index
index graphs or alignments for random access or mapping
.TP
\fB\-\-\fR map
MEM\-based read alignment
.TP
\fB\-\-\fR augment
augment a graph from an alignment
.TP
\fB\-\-\fR pack
convert alignments to a compact coverage index
.TP
\fB\-\-\fR call
call or genotype VCF variants
.TP
\fB\-\-\fR help
show all subcommands
.SS "useful graph tools:"
.TP
\fB\-\-\fR deconstruct
create a VCF from variation in the graph
.TP
\fB\-\-\fR find
use an index to find nodes, edges, kmers, paths, or positions
.TP
\fB\-\-\fR ids
manipulate node ids
.TP
\fB\-\-\fR mod
filter, transform, and edit the graph
.TP
\fB\-\-\fR prune
prune the graph for GCSA2 indexing
.TP
\fB\-\-\fR sim
simulate reads from a graph
.TP
\fB\-\-\fR snarls
compute snarls and their traversals
.TP
\fB\-\-\fR stats
metrics describing graph and alignment properties
.TP
\fB\-\-\fR view
format conversions for graphs and alignments
.SS "specialized graph tools:"
.TP
\fB\-\-\fR add
add variants from a VCF to a graph
.TP
\fB\-\-\fR align
local alignment
.TP
\fB\-\-\fR annotate
annotate alignments with graphs and graphs with alignments
.TP
\fB\-\-\fR chunk
split graph or alignment into chunks
.TP
\fB\-\-\fR circularize
circularize a path within a graph
.TP
\fB\-\-\fR combine
merge multiple graph files together
.TP
\fB\-\-\fR compare
compare the kmer space of two graphs
.TP
\fB\-\-\fR concat
concatenate graphs tail\-to\-head
.TP
\fB\-\-\fR convert
convert graphs between handle\-graph compiant formats
.TP
\fB\-\-\fR depth
estimate sequencing depth
.TP
\fB\-\-\fR dotplot
generate the dotplot matrix from the embedded paths in an xg index
.TP
\fB\-\-\fR explode
split graph into connected components
.TP
\fB\-\-\fR filter
filter reads
.TP
\fB\-\-\fR gamcompare
compare alignment positions
.TP
\fB\-\-\fR gampcompare
compare multipath alignment positions
.TP
\fB\-\-\fR gamsort
Sort a GAM file or index a sorted GAM file.
.TP
\fB\-\-\fR gbwt
Manipulate GBWTs
.TP
\fB\-\-\fR genotype
Genotype (or type) graphs, GAMS, and VCFs.
.TP
\fB\-\-\fR inject
lift over alignments for the graph
.TP
\fB\-\-\fR join
combine graphs via a new head
.TP
\fB\-\-\fR kmers
enumerate kmers of the graph
.TP
\fB\-\-\fR locify
find loci
.TP
\fB\-\-\fR mpmap
multipath alignments of reads to a graph
.TP
\fB\-\-\fR msga
multiple sequence graph alignment
.TP
\fB\-\-\fR paths
traverse paths in the graph
.TP
\fB\-\-\fR recalibrate
recalibrate mapping qualities
.TP
\fB\-\-\fR rna
construct spliced variation graphs and transcript paths
.TP
\fB\-\-\fR sift
Filter Alignments by various metrics related to variant calling.
.TP
\fB\-\-\fR simplify
graph simplification
.TP
\fB\-\-\fR sort
sort variant graph by various algorithms
.TP
\fB\-\-\fR srpe
graph\-external SV detection
.TP
\fB\-\-\fR surject
map alignments onto specific paths
.TP
\fB\-\-\fR trace
trace haplotypes
.TP
\fB\-\-\fR translate
project alignments and paths through a graph translation
.TP
\fB\-\-\fR vectorize
transform alignments to simple ML\-compatible vectors
.TP
\fB\-\-\fR viz
render visualizations of indexed graphs and read sets
.SS "developer commands:"
.TP
\fB\-\-\fR benchmark
run and report on performance benchmarks
.TP
\fB\-\-\fR bugs
show or create bugs
.TP
\fB\-\-\fR cluster
find and cluster mapping seeds
.TP
\fB\-\-\fR crash
throw an error
.TP
\fB\-\-\fR giraffe
Graph Alignment Format Fast Emitter
.TP
\fB\-\-\fR mcmc
Finds haplotypes based on reads using MCMC methods
.TP
\fB\-\-\fR minimizer
build a minimizer index
.TP
\fB\-\-\fR test
run unit tests
.TP
\fB\-\-\fR validate
validate the semantics of a graph or gam
.TP
\fB\-\-\fR version
version information
.PP
For technical support, please visit: https://www.biostars.org/t/vg/
.PP
Compiled with g++ (Debian 10.2.1\-3) 10.2.1 20201224 on Linux
Linked against libstd++ 20201224
Built by buildd@x86\-ubc\-01