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agat_sq_remove_redundant_entries.pl#

DESCRIPTION#

The script remove redundant entries: same seq_id,primary_tag,start,stop,ID,Parent. If ID and Parent attribute is not present, we do no remove the feature. If one of them do not exists we use "" instead.

SYNOPSIS#

agat_sq_remove_redundant_entries.pl -i <input file> [-o <output file>]
agat_sq_remove_redundant_entries.pl --help

OPTIONS#

  • -i, --gff, --file or --input

    STRING: Input GTF/GFF file.

  • -o or --output

    STRING: Output file. If no output file is specified, the output will be written to STDOUT. The result is in tabulate format.

  • -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).

  • --help or -h

    Display this helpful text.