GTrack - a practical unification of tabular file formats

What is GTrack?

GTrack is a general purpose, tabular file format for representing data in the form of genomic tracks, that is, as elements associated to positions along a reference (genome) sequence. 

Why GTrack?

GTrack emphasizes preciseness, flexibility, and simple parsing. This is achieved by e.g. allowing flexible columns specification (but not line-specific attributes), and declaring syntactic properties at the beginning of the file (allowing parsers to cleanly restrict support to a subset of the GTrack specification).

A main contribution by the format is the unified and optimized formalization of sequence level genomic data into one of fifteen main track types, as developed in the paper introducing the GTrack format. Together with the flexible column specification, this allows GTrack to function as a superset of several existing formats (GFF/BED/BedGraph/WIG) at the syntactic level.

Example GTrack files

The simplest form of a GTrack file merely provides chromosome/start/end values for a set of track elements (identical to the three-column BED-format):

chr1  121  201
chr2  486 1240

More information can be included by modifying the headers for column specification and/or the track type:

##Track type: valued segments
###seqid  tech       start  end   value  strand
####genome=hg19
chr1      ChIP-seq   1047   1165  0.625  -
chr2      ChIP-chip  2002   2450  .      +
chr2      ChIP-chip  3033   3246  0.355  +

GTrack specification

The most up-to-date version of the GTrack specification is available here.

GTrack tools

The following tools are available from the Genomic HyperBrowser. Just click the logo on the top of the screen, and a menu appears. The following tools are available under the header "GTrack tools":

• Show GTrack specification
• Create GTrack file from unstructured tabular data
• Expand GTrack headers
• Validate GTrack file
• Standardize GTrack file
• Sort GTrack file
• Complement GTrack columns
• Convert between GTrack/BED/WIG/bedGraph/GFF/FASTA files

GTrack subtypes 

GTrack examples from the specification 

GTrack examples from the paper 

Other GTrack examples

Examples in other formats

How to cite GTrack

If you refer to GTrack in your published work, please cite the following publication:

• Gundersen S, Kalas M, Abul O, Frigessi A, Hovig E, Sandve GK: Identifying elemental genomic track types and representing them uniformly. BMC Bioinformatics 2011, 12:494.

GTrack specification by Sveinung Gundersen, Matus Kalas, Osman Abul, Arnoldo Frigessi, Eivind Hovig, Geir Kjetil Sandve is licensed under a Creative Commons Attribution-NoDerivs 3.0 Unported License.
Permissions beyond the scope of this license may be available at www.gtrack.no.