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.