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vg version v1.22.0
February 2020


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tools for working with genome variation graphs


vg - manual page for vg version v1.22.0 "Rotella"


vg: variation graph tool, version v1.22.0 "Rotella"
usage: vg <command> [options]

main mapping and calling pipeline:

-- construct
graph construction
-- index
index graphs or alignments for random access or mapping
-- map MEM-based read alignment
-- augment
augment a graph from an alignment
-- pack convert alignments to a compact coverage index
-- call call or genotype VCF variants
-- help show all subcommands

useful graph tools:

-- deconstruct
create a VCF from variation in the graph
-- find use an index to find nodes, edges, kmers, paths, or positions
-- ids manipulate node ids
-- mod filter, transform, and edit the graph
-- prune
prune the graph for GCSA2 indexing
-- sim simulate reads from a graph
-- snarls
compute snarls and their traversals
-- stats
metrics describing graph and alignment properties
-- view format conversions for graphs and alignments

specialized graph tools:

-- add add variants from a VCF to a graph
-- align
local alignment
-- annotate
annotate alignments with graphs and graphs with alignments
-- chunk
split graph or alignment into chunks
-- circularize
circularize a path within a graph
-- combine
merge multiple graph files together
-- compare
compare the kmer space of two graphs
-- concat
concatenate graphs tail-to-head
-- convert
convert graphs between handle-graph compiant formats
-- depth
estimate sequencing depth
-- dotplot
generate the dotplot matrix from the embedded paths in an xg index
-- explode
split graph into connected components
-- filter
filter reads
-- gamcompare
compare alignment positions
-- gamsort
Sort a GAM file or index a sorted GAM file.
-- gbwt Manipulate GBWTs
-- genotype
Genotype (or type) graphs, GAMS, and VCFs.
-- inject
lift over alignments for the graph
-- join combine graphs via a new head
-- kmers
enumerate kmers of the graph
-- locify
find loci
-- mpmap
multipath alignments of reads to a graph
-- msga multiple sequence graph alignment
-- paths
traverse paths in the graph
-- recalibrate
recalibrate mapping qualities
-- rna construct spliced variation graphs and transcript paths
-- sift Filter Alignments by various metrics related to variant calling.
-- simplify
graph simplification
-- sort sort variant graph by various algorithms
-- srpe graph-external SV detection
-- surject
map alignments onto specific paths
-- trace
trace haplotypes
-- translate
project alignments and paths through a graph translation
-- vectorize
transform alignments to simple ML-compatible vectors
-- viz render visualizations of indexed graphs and read sets

developer commands:

-- benchmark
run and report on performance benchmarks
-- bugs show or create bugs
-- cluster
find and cluster mapping seeds
-- crash
throw an error
-- gaffe
Graph Alignment Format Fast Emitter
-- mcmc Finds haplotypes based on reads using MCMC methods
-- minimizer
build a minimizer index
-- test run unit tests
-- validate
validate the semantics of a graph or gam
-- version
version information
For technical support, please visit:
Compiled with g++ (Ubuntu 9.2.1-30ubuntu1) 9.2.1 20200224 on Linux Linked against libstd++ 20200224 Built by buildd@lgw01-amd64-016


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