table of contents
VG(1) | Sospiro"" | VG(1) |
NAME¶
vg - tools for working with genome variation graphs
DESCRIPTION¶
vg: variation graph tool, version v1.29.0 "Sospiro"
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
- -- gampcompare
- compare multipath 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
- -- giraffe
- 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: https://www.biostars.org/t/vg/
Compiled with g++ (Debian 10.2.1-3) 10.2.1 20201224 on Linux Linked against libstd++ 20201224 Built by buildd@x86-ubc-01
December 2020 | vg version v1.29.0 |