GFF/GTF File Format - Definition and supported options
The GFF (General Feature Format) format consists of one line per feature, each containing 9 columns of data, plus optional track definition lines. The following documentation is based on the Version 2 specifications.
The GTF (General Transfer Format) is identical to GFF version 2.
Fields must be tab-separated. Also, all but the final field in each feature line must contain a value; "empty" columns should be denoted with a '.'
- seqname - name of the chromosome or scaffold; chromosome names can be given with or without the 'chr' prefix. Important note: the seqname must be one used within Ensembl, i.e. a standard chromosome name or an Ensembl identifier such as a scaffold ID, without any additional content such as species or assembly. See the example GFF output below.
- source - name of the program that generated this feature, or the data source (database or project name)
- feature - feature type name, e.g. Gene, Variation, Similarity
- start - Start position of the feature, with sequence numbering starting at 1.
- end - End position of the feature, with sequence numbering starting at 1.
- score - A floating point value.
- strand - defined as + (forward) or - (reverse).
- frame - One of '0', '1' or '2'. '0' indicates that the first base of the feature is the first base of a codon, '1' that the second base is the first base of a codon, and so on..
- attribute - A semicolon-separated list of tag-value pairs, providing additional information about each feature.
Note that where the attributes contain identifiers that link the features together into a larger structure, these will be used by Ensembl to display the features as joined blocks.
Sample GTF output from Ensembl data dump:
1 transcribed_unprocessed_pseudogene gene 11869 14409 . + . gene_id "ENSG00000223972"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; 1 processed_transcript transcript 11869 14409 . + . gene_id "ENSG00000223972"; transcript_id "ENST00000456328"; gene_name "DDX11L1"; gene_sourc e "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-002"; transcript_source "havana";
Sample GFF output from Ensembl export:
X Ensembl Repeat 2419108 2419128 42 . . hid=trf; hstart=1; hend=21 X Ensembl Repeat 2419108 2419410 2502 - . hid=AluSx; hstart=1; hend=303 X Ensembl Repeat 2419108 2419128 0 . . hid=dust; hstart=2419108; hend=2419128 X Ensembl Pred.trans. 2416676 2418760 450.19 - 2 genscan=GENSCAN00000019335 X Ensembl Variation 2413425 2413425 . + . X Ensembl Variation 2413805 2413805 . + .
Although not part of the formal GFF specification, Ensembl uses track lines to further configure sets of features (thus maintaining compatibility with UCSC). Track lines should be placed at the beginning of the list of features they are to affect.
The track line consists of the word 'track' followed by space-separated key=value pairs - see the example below. Valid parameters used by Ensembl are:
- name - unique name to identify this track when parsing the file
- description - Label to be displayed under the track in Region in Detail
- priority - integer defining the order in which to display tracks, if multiple tracks are defined.
For more information about this file format, see the documentation on the GMOD wiki.