agat_sp_fix_cds_frame.pl
DESCRIPTION
This script aims to fix the cds phases.
SYNOPSIS
agat_sp_fix_cds_frame.pl --gff infile.gff -f fasta [ -o outfile ]
agat_sp_fix_cds_frame.pl --help
OPTIONS
-g, --gff or -ref
Input GTF/GFF file.
-fa or --fasta
Input fasta file.
-v or --verbose
Add verbosity.
-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.