AGAT a GFF/GTF toolkit allowing you to perform almost everything you might want to achieve ^^
AGAT has the power to check, fix, pad missing information (features/attributes) of any kind of GTF and GFF to create complete, sorted and standardised gff3 format. Over the years it has been enriched by many many tools to perform just about any tasks that is possible related to GTF/GFF format files (sanitizing, conversions, merging, modifying, filtering, FASTA sequence extraction, adding information, etc). Comparing to other methods AGAT is robust to even the most despicable GTF/GFF files.
Standardize/sanitize any GTF/GFF file into a comprehensive GFF3 format (script with _sp_ prefix)
task
tool
check, fix, pad missing information into sorted and standardised gff3
agat_convert_sp_gxf2gxf.pl
* add missing parent features (e.g. gene and mRNA if only CDS/exon exists).
* add missing features (e.g. exon and UTR).
* add missing mandatory attributes (i.e. ID, Parent).
* fix identifiers to be uniq.
* fix feature locations.
* remove duplicated features.
* group related features (if spread in different places in the file).
* sort features (tabix optional).
* merge overlapping loci into one single locus (only if option activated).
Convert many formats
task
tool
convert any GTF/GFF into BED format
agat_convert_sp_gff2bed.pl
convert any GTF/GFF into GTF format
agat_convert_sp_gff2gtf.pl
convert any GTF/GFF into tabulated format
agat_sp_gff2tsv.pl
convert any BAM from minimap2 into GFF format
agat_convert_sp_minimap2_bam2gff.pl
convert any GTF/GFF into ZFF format
agat_sp_gff2zff.pl
convert any GTF/GFF into any GTF/GFF (bioperl) format
agat_convert_sp_gxf2gxf.pl
convert BED format into GFF3 format
agat_convert_bed2gff.pl
convert EMBL format into GFF3 format
agat_convert_embl2gff.pl
convert genscan format into GFF3 format
agat_convert_genscan2gff.pl
convert mfannot format into GFF3 format
agat_convert_mfannot2gff.pl
Perform numerous tasks (Just about anything that is possible)