agat_sp_alignment_output_style.pl
DESCRIPTION
The script takes a normal gtf/gff annotation format file and convert it to gff3 alignment format. It means it add a structure of match / match_part as relationship between the different features.
SYNOPSIS
agat_sp_alignment_output_style.pl -g infile.gff [ -o outfile ]
agat_sp_alignment_output_style.pl --help
OPTIONS
-g, --gff or -ref
Input GTF/GFF file.
-c or --ct
When the gff file provided is not correcly formated and features are linked to each other by a comon tag (by default locus_tag), this tag can be provided to parse the file correctly.
-v
Verbose option to see the warning messages when parsing the gff file.
-o or --output
Output GFF file. If no output file is specified, the output will be written to STDOUT.
-h or --help
Display this helpful text.