vg version v1.22.0
February 2020
NAME
vg - manual page for vg version v1.22.0 "Rotella"
DESCRIPTION
vg: variation graph tool, version v1.22.0 "Rotella"
For technical support, please visit: https://www.biostars.org/t/vg/
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 |
Compiled with g++ (Ubuntu 9.2.1-30ubuntu1) 9.2.1 20200224 on Linux Linked against libstd++ 20200224 Built by buildd@lgw01-amd64-016