How to filter a gff3 file by gene IDs
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.
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You can use AGAT
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.
agat_sp_filter_feature_from_kill_list.pl --gff input.gff --kill_list file.txtthe kill list will be an ID per line
Thank you. I'll install a recent version of AGAT and then try this.
I could use this agat script from the latest agat version for the filtering.
You can use AGAT