agat_sp_filter_incomplete_gene_coding_models.pl
DESCRIPTION
The script aims to remove incomplete gene models. An incomplete gene coding model is a gene coding with start and/or stop codon missing in its cds. You can modify the behavior using the skip_start_check or skip_stop_check options.
SYNOPSIS
agat_sp_filter_incomplete_gene_coding_models.pl --gff infile.gff --fasta genome.fa [ -o outfile ]
agat_sp_filter_incomplete_gene_coding_models.pl --help
OPTIONS
-gff
Input GTF/GFF file.
-fa or --fasta
Genome fasta file. The name of the fasta file containing the genome to work with.
--ct or --table or --codon
This option allows specifying the codon table to use. It expects an integer [default 1]
--ad or --add_flag
Instead of filter the result into two output files, write only one and add the flag <incomplete> in the gff.(tag = inclomplete, value = 1, 2, 3. 1=start missing; 2=stop missing; 3=both)
--skip_start_check or --sstartc
Gene model must have a start codon. Activated by default.
--skip_stop_check or --sstopc
Gene model must have a stop codon. Activated by default.
-o , --output , --out or --outfile
Output GFF file. If no output file is specified, the output will be written to STDOUT.
-v
Verbose option, make it easier to follow what is going on for debugging purpose.
-h or --help
Display this helpful text.