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.