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agat_convert_bed2gff.pl#

DESCRIPTION#

The script takes a bed file as input, and will translate it in gff format. The BED format is described here The script converts 0-based, half-open [start-1, end) bed file to 1-based, closed [start, end] General Feature Format v3 (GFF3).

SYNOPSIS#

agat_convert_bed2gff.pl --bed infile.bed [ -o outfile ]
agat_convert_bed2gff.pl -h

OPTIONS#

  • --bed

    Input bed file that will be converted.

  • --source

    The source informs about the tool used to produce the data and is stored in 2nd field of a gff file. Example: Stringtie,Maker,Augustus,etc. [default: data]

  • --primary_tag

    The primary_tag corresponds to the data type and is stored in 3rd field of a gff file. Example: gene,mRNA,CDS,etc. [default: gene]

  • --inflate_off

    By default we inflate the block fields (blockCount, blockSizes, blockStarts) to create subfeatures of the main feature (primary_tag). The type of subfeature created is based on the inflate_type parameter. If you do not want this inflating behaviour you can deactivate it by using the --inflate_off option.

  • --inflate_type

    Feature type (3rd column in gff) created when inflate parameter activated [default: exon].

  • --verbose

    add verbosity

  • -o , --output , --out , --outfile or --gff

    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.