GFF to GTF conversion#
It exists many GFF formats and many GTF formats (see here for a complete review) and many tools to perform the conversion. We will try to see in this review the main differences.
Table of Contents#
- Test summary
- The GFF file to convert
- The converters
- AGAT
- gffread
- GenomeTools
- ea-utils
- TransDecoder
- Kent utils
- Feature types in GTF versions
Test summary#
| tool | respect GTF format | UTR conserved | attribute conserved | Stop codon removed from CDS | Comment |
|---|---|---|---|---|---|
| AGAT | Yes - All (default GTF3) | Yes it converts UTR terms to the appropriate ones according to the GTF version selected. | Yes - All | Yes (Only if the feature is present in the file. If not it is possible to add it via agat_sp_add_start_and_stop.pl) | Can take any GTF GFF as input. The only one keeping comments at the beginning of the file. |
| gffread | No - They say GTF2.2 but it is not: transcript should be removed; start_codon and stop_codon should stay. | No | No | No | |
| GenomeTools | No - only CDS and exon kept | No | No | No | gene_id and transcript_id get new identifiers. |
| ea-utils | No - only CDS and exon kept | No | No | No | |
| TransDecoder | No - start and stop codon removed | No | Name only | No | Needs the fasta file for the conversion. Location of the last CDS modified and incorrect |
| Kent utils | No - gene is missing or transcript is superfluous to be compliant to one of the GTF format | No | No | Yes | Create a new attribute 'gene_name'. |
The GFF file to convert#
The test file is a GFF3 file:
##gff-version 3
# This is a test sample
scaffold625 maker gene 337818 343277 . + . ID=CLUHARG00000005458;Name=TUBB3_2
scaffold625 maker mRNA 337818 343277 . + . ID=CLUHART00000008717;Parent=CLUHARG00000005458
scaffold625 maker tss 337916 337918 . + . ID=CLUHART00000008717:tss;Parent=CLUHART00000008717
scaffold625 maker start_codon 337916 337918 . + . ID=CLUHART00000008717:start;Parent=CLUHART00000008717
scaffold625 maker CDS 337915 337971 . + 0 ID=CLUHART00000008717:cds;Parent=CLUHART00000008717
scaffold625 maker CDS 340733 340841 . + 0 ID=CLUHART00000008717:cds;Parent=CLUHART00000008717
scaffold625 maker CDS 341518 341628 . + 2 ID=CLUHART00000008717:cds;Parent=CLUHART00000008717
scaffold625 maker CDS 341964 343033 . + 2 ID=CLUHART00000008717:cds;Parent=CLUHART00000008717
scaffold625 maker stop_codon 343031 343033 . + . ID=CLUHART00000008717:stop;Parent=CLUHART00000008717
scaffold625 maker exon 337818 337971 . + . ID=CLUHART00000008717:exon1;Parent=CLUHART00000008717
scaffold625 maker exon 340733 340841 . + . ID=CLUHART00000008717:exon2;Parent=CLUHART00000008717
scaffold625 maker exon 341518 341628 . + . ID=CLUHART00000008717:exon3;Parent=CLUHART00000008717
scaffold625 maker exon 341964 343277 . + . ID=CLUHART00000008717:exon4;Parent=CLUHART00000008717
scaffold625 maker five_prime_utr 337818 337914 . + . ID=CLUHART00000008717:five_prime_utr;Parent=CLUHART00000008717
scaffold625 maker three_prime_UTR 343034 343277 . + . ID=CLUHART00000008717:three_prime_utr;Parent=CLUHART00000008717
The converters#
AGAT#
AGAT v0.5.1
agat_convert_sp_gff2gtf.pl --gff 1_test.gff -o 1_test_agat.gtf
##gtf-version 3
##This is a test sample
scaffold625 maker gene 337818 343277 . + . gene_id "CLUHARG00000005458"; ID "CLUHARG00000005458"; Name "TUBB3_2";
scaffold625 maker transcript 337818 343277 . + . gene_id "CLUHARG00000005458"; transcript_id "CLUHART00000008717"; ID "CLUHART00000008717"; Parent "CLUHARG00000005458"; original_biotype "mrna";
scaffold625 maker exon 337818 337971 . + . gene_id "CLUHARG00000005458"; transcript_id "CLUHART00000008717"; ID "CLUHART00000008717:exon1"; Parent "CLUHART00000008717";
scaffold625 maker exon 340733 340841 . + . gene_id "CLUHARG00000005458"; transcript_id "CLUHART00000008717"; ID "CLUHART00000008717:exon2"; Parent "CLUHART00000008717";
scaffold625 maker exon 341518 341628 . + . gene_id "CLUHARG00000005458"; transcript_id "CLUHART00000008717"; ID "CLUHART00000008717:exon3"; Parent "CLUHART00000008717";
scaffold625 maker exon 341964 343277 . + . gene_id "CLUHARG00000005458"; transcript_id "CLUHART00000008717"; ID "CLUHART00000008717:exon4"; Parent "CLUHART00000008717";
scaffold625 maker CDS 337915 337971 . + 0 gene_id "CLUHARG00000005458"; transcript_id "CLUHART00000008717"; ID "CLUHART00000008717:cds"; Parent "CLUHART00000008717";
scaffold625 maker CDS 340733 340841 . + 0 gene_id "CLUHARG00000005458"; transcript_id "CLUHART00000008717"; ID "CLUHART00000008717:cds"; Parent "CLUHART00000008717";
scaffold625 maker CDS 341518 341628 . + 2 gene_id "CLUHARG00000005458"; transcript_id "CLUHART00000008717"; ID "CLUHART00000008717:cds"; Parent "CLUHART00000008717";
scaffold625 maker CDS 341964 343030 . + 2 gene_id "CLUHARG00000005458"; transcript_id "CLUHART00000008717"; ID "CLUHART00000008717:cds"; Parent "CLUHART00000008717";
scaffold625 maker five_prime_utr 337818 337914 . + . gene_id "CLUHARG00000005458"; transcript_id "CLUHART00000008717"; ID "CLUHART00000008717:five_prime_utr"; Parent "CLUHART00000008717";
scaffold625 maker start_codon 337916 337918 . + . gene_id "CLUHARG00000005458"; transcript_id "CLUHART00000008717"; ID "CLUHART00000008717:start"; Parent "CLUHART00000008717";
scaffold625 maker stop_codon 343031 343033 . + . gene_id "CLUHARG00000005458"; transcript_id "CLUHART00000008717"; ID "CLUHART00000008717:stop"; Parent "CLUHART00000008717";
scaffold625 maker three_prime_utr 343034 343277 . + . gene_id "CLUHARG00000005458"; transcript_id "CLUHART00000008717"; ID "CLUHART00000008717:three_prime_utr"; Parent "CLUHART00000008717"; original_biotype "three_prime_UTR";
gffread#
gffread 0.11.4
gffread -E 1_test.gff -T -o 1_test_gffread.gtf
scaffold625 maker transcript 337818 343277 . + . transcript_id "CLUHART00000008717"; gene_id "CLUHARG00000005458";
scaffold625 maker exon 337818 337971 . + . transcript_id "CLUHART00000008717"; gene_id "CLUHARG00000005458";
scaffold625 maker exon 340733 340841 . + . transcript_id "CLUHART00000008717"; gene_id "CLUHARG00000005458";
scaffold625 maker exon 341518 341628 . + . transcript_id "CLUHART00000008717"; gene_id "CLUHARG00000005458";
scaffold625 maker exon 341964 343277 . + . transcript_id "CLUHART00000008717"; gene_id "CLUHARG00000005458";
scaffold625 maker CDS 337915 337971 . + 0 transcript_id "CLUHART00000008717"; gene_id "CLUHARG00000005458";
scaffold625 maker CDS 340733 340841 . + 0 transcript_id "CLUHART00000008717"; gene_id "CLUHARG00000005458";
scaffold625 maker CDS 341518 341628 . + 2 transcript_id "CLUHART00000008717"; gene_id "CLUHARG00000005458";
scaffold625 maker CDS 341964 343033 . + 2 transcript_id "CLUHART00000008717"; gene_id "CLUHARG00000005458";
GenomeTools#
GenomeTools 1.6.1
The help says it convert into GTF2.2
gt gff3_to_gtf 1_test.gff > 1_test_genometools.gtf
scaffold625 maker exon 337818 337971 . + . gene_id "1"; transcript_id "1.1";
scaffold625 maker exon 340733 340841 . + . gene_id "1"; transcript_id "1.1";
scaffold625 maker exon 341518 341628 . + . gene_id "1"; transcript_id "1.1";
scaffold625 maker exon 341964 343277 . + . gene_id "1"; transcript_id "1.1";
scaffold625 maker CDS 337915 337971 . + 0 gene_id "1"; transcript_id "1.1";
scaffold625 maker CDS 340733 340841 . + 0 gene_id "1"; transcript_id "1.1";
scaffold625 maker CDS 341518 341628 . + 2 gene_id "1"; transcript_id "1.1";
scaffold625 maker CDS 341964 343033 . + 2 gene_id "1"; transcript_id "1.1";
ea-utils#
ea-utils commit 2b3d8c5d148801c98a2b3f3d54009a72c5b99521
./gff2gtf-eautils test_1.gff > 1_test_ea-utils.gtf
scaffold625 maker exon 337818 337971 0 + . gene_id "CLUHARG00000005458"; transcript_id "CLUHART00000008717:CLUHARG00000005458";
scaffold625 maker CDS 337915 337971 0 + 0 gene_id "CLUHARG00000005458"; transcript_id "CLUHART00000008717:CLUHARG00000005458";
scaffold625 maker CDS 340733 340841 0 + 0 gene_id "CLUHARG00000005458"; transcript_id "CLUHART00000008717:CLUHARG00000005458";
scaffold625 maker exon 340733 340841 0 + . gene_id "CLUHARG00000005458"; transcript_id "CLUHART00000008717:CLUHARG00000005458";
scaffold625 maker CDS 341518 341628 0 + 2 gene_id "CLUHARG00000005458"; transcript_id "CLUHART00000008717:CLUHARG00000005458";
scaffold625 maker exon 341518 341628 0 + . gene_id "CLUHARG00000005458"; transcript_id "CLUHART00000008717:CLUHARG00000005458";
scaffold625 maker CDS 341964 343033 0 + 2 gene_id "CLUHARG00000005458"; transcript_id "CLUHART00000008717:CLUHARG00000005458";
scaffold625 maker exon 341964 343277 0 + . gene_id "CLUHARG00000005458"; transcript_id "CLUHART00000008717:CLUHARG00000005458";
TransDecoder#
Transdecoder v5.5.0
gff3_gene_to_gtf_format.pl test_1.gff test_1.fa > 1_test_transdecoder.gtf
scaffold625 maker gene 337818 343277 0 + . gene_id "CLUHARG00000005458"; Name "TUBB3_2";
scaffold625 maker transcript 337818 343277 0 + . gene_id "CLUHARG00000005458"; transcript_id "CLUHART00000008717"; Name "TUBB3_2";
scaffold625 maker exon 337818 337971 0 + . gene_id "CLUHARG00000005458"; transcript_id "CLUHART00000008717"; Name "TUBB3_2";
scaffold625 maker CDS 337818 337971 0 + . gene_id "CLUHARG00000005458"; transcript_id "CLUHART00000008717"; Name "TUBB3_2";
scaffold625 maker exon 340733 340841 0 + . gene_id "CLUHARG00000005458"; transcript_id "CLUHART00000008717"; Name "TUBB3_2";
scaffold625 maker CDS 340733 340841 0 + . gene_id "CLUHARG00000005458"; transcript_id "CLUHART00000008717"; Name "TUBB3_2";
scaffold625 maker exon 341518 341628 0 + . gene_id "CLUHARG00000005458"; transcript_id "CLUHART00000008717"; Name "TUBB3_2";
scaffold625 maker CDS 341518 341628 0 + . gene_id "CLUHARG00000005458"; transcript_id "CLUHART00000008717"; Name "TUBB3_2";
scaffold625 maker exon 341964 343277 0 + . gene_id "CLUHARG00000005458"; transcript_id "CLUHART00000008717"; Name "TUBB3_2";
scaffold625 maker CDS 341964 343277 0 + . gene_id "CLUHARG00000005458"; transcript_id "CLUHART00000008717"; Name "TUBB3_2";
Kent utils#
version from 26-Feb-2020
./gff3ToGenePred.dms 1_test.gff temp.genePred ./genePredToGtf.dms file temp.genePred 1_test_genePred.gtf
scaffold625 temp.genePred transcript 337818 343277 . + . gene_id "CLUHARG00000005458"; transcript_id "CLUHART00000008717"; gene_name "CLUHARG00000005458";
scaffold625 temp.genePred exon 337818 337971 . + . gene_id "CLUHARG00000005458"; transcript_id "CLUHART00000008717"; exon_number "1"; exon_id "CLUHART00000008717.1"; gene_name "CLUHARG00000005458";
scaffold625 temp.genePred CDS 337915 337971 . + 0 gene_id "CLUHARG00000005458"; transcript_id "CLUHART00000008717"; exon_number "1"; exon_id "CLUHART00000008717.1"; gene_name "CLUHARG00000005458";
scaffold625 temp.genePred exon 340733 340841 . + . gene_id "CLUHARG00000005458"; transcript_id "CLUHART00000008717"; exon_number "2"; exon_id "CLUHART00000008717.2"; gene_name "CLUHARG00000005458";
scaffold625 temp.genePred CDS 340733 340841 . + 0 gene_id "CLUHARG00000005458"; transcript_id "CLUHART00000008717"; exon_number "2"; exon_id "CLUHART00000008717.2"; gene_name "CLUHARG00000005458";
scaffold625 temp.genePred exon 341518 341628 . + . gene_id "CLUHARG00000005458"; transcript_id "CLUHART00000008717"; exon_number "3"; exon_id "CLUHART00000008717.3"; gene_name "CLUHARG00000005458";
scaffold625 temp.genePred CDS 341518 341628 . + 2 gene_id "CLUHARG00000005458"; transcript_id "CLUHART00000008717"; exon_number "3"; exon_id "CLUHART00000008717.3"; gene_name "CLUHARG00000005458";
scaffold625 temp.genePred exon 341964 343277 . + . gene_id "CLUHARG00000005458"; transcript_id "CLUHART00000008717"; exon_number "4"; exon_id "CLUHART00000008717.4"; gene_name "CLUHARG00000005458";
scaffold625 temp.genePred CDS 341964 343030 . + 2 gene_id "CLUHARG00000005458"; transcript_id "CLUHART00000008717"; exon_number "4"; exon_id "CLUHART00000008717.4"; gene_name "CLUHARG00000005458";
scaffold625 temp.genePred start_codon 337915 337917 . + 0 gene_id "CLUHARG00000005458"; transcript_id "CLUHART00000008717"; exon_number "1"; exon_id "CLUHART00000008717.1"; gene_name "CLUHARG00000005458";
scaffold625 temp.genePred stop_codon 343031 343033 . + 0 gene_id "CLUHARG00000005458"; transcript_id "CLUHART00000008717"; exon_number "4"; exon_id "CLUHART00000008717.4"; gene_name "CLUHARG00000005458";
Feature types in GTF versions#
| GTF version | feature type accepted |
|---|---|
| GTF3 | gene, transcript, exon, CDS, Selenocysteine, start_codon, stop_codon, three_prime_utr, five_prime_utr |
| GTF2_5 | gene, transcript, exon, CDS, UTR, start_codon, stop_codon, Selenocysteine |
| GTF2_2 | CDS, start_codon, stop_codon, 5UTR, 3UTR, inter, inter_CNS, intron_CNS, exon |
| GTF2_1 | CDS, start_codon, stop_codon, exon, 5UTR, 3UTR |
| GTF2 | CDS, start_codon, stop_codon, exon |
| GTF1 | CDS, start_codon, stop_codon, exon, intron |