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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