agat_sq_filter_feature_from_fasta.pl

DESCRIPTION

This script is a kind of annotation filter by sequence name. It goes through the gff annotation features and remove those that are not linked to a sequence from the fasta file provided. The match between sequence name in the fasta file and the 1st column of the gff3 file is case sensitive.

SYNOPSIS

agat_sq_filter_feature_from_fasta.pl --gff <gff_file.gff> --fasta <fasta_file.fa> [-o <output file>]
agat_sq_filter_feature_from_fasta.pl --help

OPTIONS

  • --gff, --file or --input

    STRING: Input GTF/GFF file.

  • -f or --fasta

    STRING: fasta file.

  • -v or --verbose

    For verbosity

  • -o or --output

    STRING: Output file. If no output file is specified, the output will be written to STDOUT. The result is in tabulate format.

  • --help or -h

    Display this helpful text.