The script aims to convert any GTF/GFF file into a proper GTF file. Full information about the format can be found here: https://github.com/NBISweden/GAAS/blob/master/annotation/knowledge/gxf.md You can choose among 6 different GTF types (1, 2, 2.1, 2.2, 2.5, 3). Depending the version selected the script will filter out the features that are not accepted. For GTF2.5 and 3, every level1 feature (e.g nc_gene pseudogene) will be converted into gene feature and every level2 feature (e.g mRNA ncRNA) will be converted into transcript feature. You can even produce a GFF-like GTF using the --relax option. It allows to keep all original feature types (3rd column).
To be fully GTF compliant all feature have a gene_id and a transcript_id attribute. The gene_id is unique identifier for the genomic source of the transcript, which is used to group transcripts into genes. The transcript_id is a unique identifier for the predicted transcript, which is used to group features into transcripts.
agat_convert_sp_gff2gtf.pl --gff infile.gtf [ -o outfile ] agat_convert_sp_gff2gtf -h
--gff or --in
Input GFF file that will be read
--gtf_version version of the GTF output. Default 3 (for GTF3)
GTF3 (9 feature types accepted): gene, transcript, exon, CDS, Selenocysteine, start_codon, stop_codon, three_prime_utr and five_prime_utr
GTF2.5 (8 feature types accepted): gene, transcript, exon, CDS, UTR, start_codon, stop_codon, Selenocysteine
GTF2.2 (9 feature types accepted): CDS, start_codon, stop_codon, 5UTR, 3UTR, inter, inter_CNS, intron_CNS and exon
GTF2.1 (6 feature types accepted): CDS, start_codon, stop_codon, exon, 5UTR, 3UTR
GTF2 (4 feature types accepted): CDS, start_codon, stop_codon, exon
GTF1 (5 feature types accepted): CDS, start_codon, stop_codon, exon, intron
Relax option avoid to apply strict GTF format specification. All feature type will be kept. No modification e.g. mRNA to transcript. No filtering i.e. feature type not accepted by GTF format are kept. gene_id and transcript_id attributes will be added, and the attributes will follow the GTF formating.
-o , --output , --out , --outfile or --gtf
Output GTF file. If no output file is specified, the output will be written to STDOUT.
-h or --help
Display this helpful text.