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

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 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 1.6.1The 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