How can I merge SQANTI3-filtered novel isoforms into a GENCODE v47 GTF?

[zhongguozhiwang]

Hello,

I have two GTFs:

• A novel-isoform file from SQANTI3 (sample.filtered_lite.gtf)
• The official GENCODE v47 annotation (gencode.v47.annotation.gtf)

A simple cat merge causes gene_id/transcript_id collisions and downstream parsing errors. Could anyone recommend:

• Tools or workflows to merge reference + novel GTFs without ID conflicts

Thank you very much for your help!