The script aims to keep records based on a keeplist. The default behaviour is to look at the features's ID. If the feature has an ID (case insensitive) listed among the keeplist it will be kept along with all related features (the whole record is kept. A record repsent all features linked by relationship e.g. gene+transcript+exon+cds of a same locus).

SYNOPSIS --gff infile.gff --keep_list file.txt  [ --output outfile ] --help


  • -f, --reffile, --gff or -ref

    Input GFF3 file that will be read

  • -p, --type or -l

    primary tag option, case insensitive, list. Allow to specied the feature types that will be handled. You can specified a specific feature by given its primary tag name (column 3) as: cds, Gene, MrNa You can specify directly all the feature of a particular level: level2=mRNA,ncRNA,tRNA,etc level3=CDS,exon,UTR,etc By default all feature are taking into account. fill the option by the value "all" will have the same behaviour.

  • --kl or --keep_list

    Keep list. One value per line.

  • -a or --attribute

    Attribute tag to specify the attribute to analyse. Case sensitive. Default: ID

  • -o or --output

    Output GFF file. If no output file is specified, the output will be written to STDOUT.

  • -v

    Verbose option for debugging purpose.

  • -c or --config

    String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently).

  • -h or --help

    Display this helpful text.