agat_sp_merge_annotations.pl

DESCRIPTION

This script merge different gff annotation files in one. It uses the AGAT parser that takes care of duplicated names and fixes other oddities met in those files.

SYNOPSIS

agat_sp_merge_annotations.pl --gff infile1 --gff infile2 --out outFile
agat_sp_merge_annotations.pl --help

OPTIONS

  • --gff or -f

    Input GTF/GFF file(s). You can specify as much file you want like so: -f file1 -f file2 -f file3

  • --out, --output or -o

    Output gff3 file where the gene incriminated will be write.

  • -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.