How to filter a gff3 file by gene IDs

Question

[William]

How to filter a gff3 file by gene IDs?

Just grepping on the IDs does output the exons and other features that are below the gene.

I thought this would be a common use case.

But can't find a command line tool that can filter a gff3 file based on IDs provided on the CLI or in a file.

[Juke34]

You can use AGAT

[William]

I looked at the AGAT documentation. But I could not find a AGAT command that could do this filtering. Can you share which command to use, with which options. Thank you.

[Juke34]

agat_sp_filter_feature_from_kill_list.pl --gff input.gff --kill_list file.txt
the kill list will be an ID per line

[William]

I could use this agat script from the latest agat version for the filtering.

[William]

Thank you. I'll install a recent version of AGAT and then try this.

[Juke34]

You can use AGAT