Coordinate Manipulation

Perform manipulations and transformations of coordinate interval files (e.g. expansion, sort, filter, convert).

Tool Name	Input	Output	Description
expand-bed	BED	BED	Expands input BED file by adding positions to the border or around the center.
expand-gff	GFF	GFF	Expands input GFF file by adding positions to the border or around the center.
bed-to-gff	BED	GFF	Converts BED file format to GFF file format.
gff-to-bed	GFF	BED	Converts GFF file format to BED file format.
sort-bed	BED + CDT	BED + CDT	Sort a CDT file and its corresponding BED file by the total score in the CDT file across the specified interval.
sort-gff	GFF + CDT	GFF + CDT	Sort a CDT file and its corresponding GFF file by the total score in the CDT file across the specified interval.
shift-coord	GFF or BED	GFF or BED	Shift the coordinate intervals within a BED or GFF file (both start and stop) by a user specified distance up or downstream.