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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:

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

useful graph tools:

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

specialized graph tools:

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

developer commands:

run and report on performance benchmarks
show or create bugs
find and cluster mapping seeds
throw an error
Graph Alignment Format Fast Emitter
Finds haplotypes based on reads using MCMC methods
build a minimizer index
run unit tests
validate the semantics of a graph or gam
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