File Types

Glossary of vg-related File Types

The vg ecosystem uses a lot of file formats. Some are new and not consistently used yet, and some are old and still required for some less-popular operations.

Some of these are described in more detail at File Formats and Index Types.

Reference Formats

These formats store genome references that define spaces in which genomics can be done.

Name	Description	Extension	Status	Notes
VG Protobuf	The original vg graph format	.vg	Conditionally useful	Can also be used to store paths without the nodes and edges they belong to. Default output format of vg construct in vg v1.40.0, since it can be generated incrementally. Can be concatenated with cat. Usually block-GZIP compressed, but some old files aren't. Consists of count-prefixed groups of length-prefixed Protobuf messages, where a string type tag takes the place of the first message in each group.
GBZ	"GBZ" graph, a compressed format storing a graph as traversed by sample haplotypes	.gbz	Recommended	Stores not only the graph but also large numbers of haplotypes, so you don't need an additional GBWT file. Internally, stores a GBWT and a GBWTGraph. Can't store edges that are not followed.
GFA	Graphical Fragment Assembly: a text-based format for storing graphs and their embedded paths.	.gfa	Recommended for interchange	vg uses GFA 1.x and doesn't really support GFA 2.
HashGraph	Graph format based on a hashtable, from libbdsg.	.hg, .vg	Recommended	Default output format of many vg subcommands as of v1.40.0.
PackedGraph	Graph format based on succinct data structures, from libbdsg.	.pg, .vg	Recommended for large graphs	This format can store graphs in less space than HashGraph, but is also slower and more complicated.
Memory-Mapped PackedGraph	A version of PackedGraph that can be incrementally read from disk	.mpg?	Experimental	Might not actually be adopted; GBZ solves a different but often more important problem
ODGI (vg flavor)	"Optimized Dynamic Genome/Graph Implementation" format.	.odgi	Removed	vg used to support a version implemented in libbdsg, which was NOT wire-compatible with the version implemented in the odgi project, and so was removed.
XG	Compressed, immutable graph format. Doesn't really stand for anything.	.xg	Conditionally useful	PackedGraph may be better, but many tools reference "xg files" as historically this was the only practical format for whole-genome graphs.
GBWTGraph	Supplemental information to turn a GBWT into a graph.	.gg	Deprecated	Stores node sequences only; defines a graph when used together with a GBWT file of haplotypes.
VG JSON	This is the VG Protobuf format, with the Protobuf Graph objects represented as JSON.	.json	Conditionally useful	Useful for exporting small graphs for analysis with jq, or importing graphs from tools that can't use libbdsg or libvgio. Generally GFA should be used instead.
Indexed VG Protobuf	This is the VG Protobuf format, stored in a sorted order with an auxilliary index file for random access.	.sorted.vg	Deprecated	Was never very popular, and Memory-Mapped PackedGraph is intended as a replacement.
FASTA	"FASTA" format for storing DNA sequences	.fa, .fasta, .fna	Recommended for linear references	This is a linear genome reference format that vg construct can consume.

Read and Alignment Formats

These formats store short or long reads from DNA sequencing machines, and can describe how they fit into references.

Name	Description	Extension	Status	Notes
GAM Protobuf	Graph Alignment/Map, vg's main format for aligned reads	.gam	Recommended
GAF	Graph Alignment Format, a text-based format for aligned reads	.gaf	Recommended for interchange	See Graph Alignment Format in vg for notes on tag meanings. In particular, vg uses the cs tag "difference string" instead of a CIGAR.
Sorted GAM	GAM file with reads sorted by graph node ID. Useful for random access with an index.	.sorted.gam	Recommended
GAM JSON	JSON version of the Protobuf GAM format.	.json	Conditionally useful	Used for analyzing reads with jq.
GAMP Protobuf	Multi-path alignment version of GAM	.gamp	Recommended
GAMP JSON	JSON version of GAMP format	.json	Conditionally useful
BAM	Binary Alignment/Map format for alignments against a linear reference	.bam	Recommended
SAM	Sequence/Alignment Map format, a text-based version of BAM	.sam	Recommended
FASTQ	Version of FASTA with per-base quality scores. Used for unaligned reads.	.fq, .fastq	Recommended

Sample Information Formats

These formats can describe individual people or other organisms and how their genomes fit into or differ from references.

Name	Description	Extension	Status	Notes
GBWT	Graph Burrows-Wheeler Transform file, storing haplotypes for samples	.gbwt	Conditionally useful	It sometimes makes more sense to use a GBZ.
GBZ	See above under Reference Formats
VCF	Variant Call Format file, storing sample genotypes and haplotypes against a linear reference	.vcf, .vcf.gz	Recommended	Not all VCF 4.3 features are supported by vg
Pack File	Stores read information as counts of visited graph elements	.cx	Recommended
Pileup Protobuf	Stores read information as counts of visited graph elements	.pileup?	Deprecated
Pileup JSON	JSON version of the Pileup Protobuf format	.json	Deprecated
Locus Protobuf	Stores genotypes against a graph reference	.loci	Experimental
Locus JSON	JSON version of the Locus Protobuf format	.json	Deprecated

Miscellaneous Formats

These formats store other kinds of information, or are precomputed indexes to speed up operations on other data.

Name	Description	Extension	Status	Notes
Distance Index (v1)	Index for computing distances between points in a graph	.dist	Deprecated	Used in vg giraffe
Distance Index (v2)	Index for computing distances between points in a graph	.dist	Recommended
GCSA	Generalized Compressed Suffix Array, version 2, for finding substrings in a graph	.gcsa	Recommended	Used in vg map and vg mpmap
Minimizer Index	Used to find "minimizer" substrings in a graph	.min	Recommended	Used in vg giraffe
BED	Browser Extensible Data format, used for defining regions	.bed	Recommended
Dot	GraphViz input format	.dot	Conditionally useful	vg view -d can export graphs in Dot format for visualization with GraphViz's dot tool.
Snarl Protobuf	Hierarchical decomposition of a graph into variable sites, called "snarls"	.snarls	Recommended
Snarl JSON	JSON representation of Protobuf snarl data	.json	Conditionally useful
SnarlTraversal Protobuf	Binary representation of possible paths through snarls	.trav?	Conditionally useful
SnarlTraversal JSON	Text representation of possible paths through snarls	.json	Conditionally useful
Node ID Translation	Recorded information about changes made to nodes while modifying a graph	.trans	Conditionally useful
VG Protobuf Index	Index over a sorted VG Protobuf file	.vgi	Experimental
GAM Index	Index over a sorted GAM Protobuf file	.gai, .gam.index	Recommended	Useful for vg chunk to fetch out reads for a particular region
FASTA Index	Index over a FASTA file for random access	.fai	Recommended
BAM Index	Index over a sorted BAM file for random access	.bai	Recommended
Tabix VCF Index	Index over a sorted, compressed VCF file for random access	.tbi	Recommended
Zipcodes	Store supplemental distance information for positions on a graph	'.zipcodes'	Experimental