bedutils / tofasta

Extract BED regions from a reference FASTA file.

Note: Sequences that are extracted will be in the same orientation as the
BED region, unless the {-ns} option is given.

Usage: bedutils tofasta {-min size} {-name} {-ns} bedfile ref.fasta

Outputs the sequences of each BED region to FASTA format.

-min    The minumum size of a region

-name   Include the name field of the BED region in the FASTA sequence name
        If used, the final name will be in the form:

        The default is to not include the BED region name (only the genomic
        coordinates will be exported).

-ns     Ignore the strand of a region (always return seq from the + strand)