GFF/GTF

A General Feature Format (GFF) file is a simple tab-delimited text file for describing genomic features. There are several slightly but significantly different GFF file formats. IGV supports the GFF2, GFF3 and GTF file formats.

• GFF2 files must have a .gff file extension for IGV. See the Wellcome Trust Sanger Institute web site (http://www.sanger.ac.uk/Software/formats/GFF/GFF_Spec.shtml) for a description of the GFF2 file format.
• GFF3 files must have a .gff3 file extension for IGV. See the Sequence Ontology Project (SO) web site (http://www.sequenceontology.org/gff3.shtml) for a description of the GFF3 file format.
• GTF files must have a .gtf file extension for IGV. See the Computational Genomics Laboratory web site (http://mblab.wustl.edu/GTF2.html) for a description of the GTF file format.

One-based index: Start and end positions are identified using a one-based index. The end position is included. For example, setting start-end to 1-2 describes two bases, the first and second in the sequence.

Display settings: To modify IGV's default display settings for the .gff or .gff3 data, include a track line in the file.

Feature display name: To override the default setting for which field is used to label the features in the IGV track, add the following line to the file:

##displayName=<field name>

Coloring features: To specify a color for a given feature, you can add this to the file as shown in the following example. Color values can be in either hexadecimal or RGB (r, g, b) format.

##gff-version 3
chr1 varclass variants_454HCDiffs 59133 59133 33 . . Var=A->G;AA=S->S;depth=9;frame=+1;gene=OR4F5;ref=novel;InRegion;color=#0000EE
chr1 varclass variants_454HCDiffs 59374 59374 67 . . Var=A->G;AA=T->A;depth=30;frame=+1;gene=OR4F5;ref=rs2691305;InRegion;color=#EE0000
chr1 varclass variants_454HCDiffs 731442 731442 100 . . Var=T->C;AA=->;depth=3;frame=;gene=;ref=rs3115865,rs61770168;OutOfRegion;color=#AAAAAA