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.

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.

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