NAME

       vg - tools for working with genome variation graphs

DESCRIPTION

       vg: variation graph tool, version v1.30.0 "Carentino"

       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

       -- giraffe
              fast haplotype-aware short 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:
       -- autoindex
              produce indexes for other subcommands

       -- deconstruct
              create a VCF from variation in the graph

       -- gbwt
              build and manipulate GBWTs

       -- ids manipulate node ids

       -- minimizer
              build a minimizer index or a syncmer index

       -- 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

       -- 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

       -- filter
              filter reads

       -- gamcompare
              compare alignment positions

       -- gampcompare
              compare multipath alignment positions

       -- gamsort
              Sort a GAM file or index a sorted GAM file.

       -- genotype
              Genotype (or type) graphs, GAMS, and VCFs.

       -- inject
              lift over alignments for the graph

       -- mpmap
              multipath alignments of reads to a graph

       -- paths
              traverse paths in the graph

       -- rna construct spliced variation graphs and transcript paths

       -- simplify
              graph simplification

       -- surject
              map alignments onto specific paths

       -- trace
              trace haplotypes

       -- 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

       -- cluster
              find and cluster mapping seeds

       -- find
              use an index to find nodes, edges, kmers, paths, or positions

       -- mcmc
              Finds haplotypes based on reads using MCMC methods

       -- test
              run unit tests

       -- validate
              validate the semantics of a graph or gam

       -- version
              version information

       For technical support, please visit: https://www.biostars.org/t/vg/

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       libstd++ 20210121 Built by buildd@lgw01-amd64-038