gtfutils / tobed

Convert a GFF/GTF file to BED format

This will convert whole genes, individual exons, or expressed regions.
Expressed regions are distinct sections of exons that take into account
alternative splicing, such that each region is assigned to be 'constant' or

Usage: gtfutils tobed [type] filename.gtf{.gz}

Where type is one of:
    -genes    The gene from start to end (including introns)
    -exons    Each annotated exon
    -introns  Each annotated intron
    -regions  Export constant / alternative regions (annotated spliced regions)
    -tss      Transcription start sites (unique)
    -txs      Transcription stop sites (unique)
    -tlss     Translational start sites (unique start codons)
    -tlxs     Translational stop sites (unique stop codons)
    -junc5    Splice junction 5' donor
    -junc3    Splice junction 3' acceptor
    -utr5     5' UTR (including introns)
    -utr3     3' UTR (including introns)

    -promoter length    Promoter region from the gene [length] upstream of TSS
                        Note: Length may also be in the form "up,down", where
                        the promoter coordinates will be TSS-up -> TSS+down.

                        By default the "down" length is zero.

                        For example, for a gene that starts a chr1:1000 (+), using
                        "-promoter 200,100" would yield a BED region of:
                        chr1   800    1100