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<code>agat_convert_sp_gff2gtf</code> introduces duplicate transcript_id, and <code>agat_sp_statistics</code> counts it twice

Status: Open.

#571 In NBISweden/AGAT;

· TomHarrop opened on Dec 11, 2025

Use of uninitialized value in concatenation (.) or string at /usr/local/bin/agat_sp_flag_premature_stop_codons.pl line 166.

Status: Open.

#570 In NBISweden/AGAT;

· fuesseler opened on Dec 4, 2025

gff Longest-CDS per gene extraction misses genes/BUSCOs

Status: Open.

#569 In NBISweden/AGAT;

· desmodus1984 opened on Nov 28, 2025

Potential problem when extracting sequences

Status: Open.

#568 In NBISweden/AGAT;

· filonico opened on Nov 20, 2025

"intron/exon"" Features locations are duplicated - consider merging qualifiers, unable to remove it.

Status: Open.

#567 In NBISweden/AGAT;

· kumariindu-commits opened on Nov 13, 2025

agat_sp_extract_sequences.pl different gffread

Status: Open.

#566 In NBISweden/AGAT;

· WWz33 opened on Oct 26, 2025

longest exon per gene above a threshold length

Status: Open.

#565 In NBISweden/AGAT;

· bioinfowheat opened on Oct 20, 2025

200k UTR created- is gff annotation or Agat correct?

Status: Open.

#563 In NBISweden/AGAT;

· desmodus1984 opened on Oct 8, 2025

introns are lost in GFF3 to GTF2.2 conversion

Status: Open.

#562 In NBISweden/AGAT;

· mrbertp opened on Oct 6, 2025

[BUG] GTF 'description' is not preserved during conversion.

Status: Open.

#561 In NBISweden/AGAT;

· marcguery opened on Sep 18, 2025

Feature request: Slight update to GTF 2.5 (GENCODE) format

Status: Open.

#560 In NBISweden/AGAT;

· mrendleman opened on Sep 17, 2025

empty attributes are appended to feature ID

Status: Open.

#556 In NBISweden/AGAT;

· Rik-149 opened on Aug 21, 2025