gtfutils

General
	add_isoform	Appends isoform annotation from UCSC isoforms file
	add_reflink	Appends isoform/name annotation from RefSeq/refLink
	add_xref	Appends name annotation from UCSC Xref file
	annotate	Annotates genomic positions based on a GTF model
	filter	Filter annotations from a GTF file
	genesize	Extract genomic/transcript sizes for genes
	junctions	Build a junction library from FASTA and GTF model
	query	Query a GTF file by coordinates
	remove_dup	Removes "_dup" entries from a GTF file (experimental)
Conversion
	fromgff	Converts a GFF annotation file to GTF (experimental)
	tobed	Convert a GFF/GTF file to BED format