The script masks (hard or soft) GFF-denoted segments out of a FASTA format file. It needs 3 input parameters: a gff3 file, a fasta file, and a Mask method. The result is written to the specified output file, or to STDOUT.

SYNOPSIS -g infile.gff -f infile.fasta  (-hm or -sm) [ -o outfile ] --help


  • -g, --gff or -ref

    Input GTF/GFF file.

  • -f or --fasta

    Input fasta file that will be masked

  • -sm

    SoftMask option =>Sequences masked will be in lowercase

  • -hm

    HardMask option => Sequences masked will be replaced by a character. By default the character used is 'n'. But you are allowed to speceify any character of your choice. To use 'z' instead of 'n' type: -hm z

  • -o or --output

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

  • -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.