Convert GFF to BED

Converts GFF file format to BED file format

File input (GFF)

This script processes GFF-type files so make sure your input is properly formatted and uses the appropriate .gff/.gtf extension if you are working from the GUI.

Output (BED)

The converted file is named the same as its corresponding input filename by default (just swap extension for .bed) in BED-style format with the details (9th) column in the GFF file used for details stored as the id column (4th) in the new BED file. Score columns map accordingly.

Output GZip

Toggling this allows the user to write output to a compressed file format using a general compression (gzip) which has the added advantage of speeding up the execution time by shrinking the I/O load (esp for large output). The .gz extension will be appended as appropriate.

Command Line Interface

Usage:

java -jar ScriptManager.jar coordinate-manipulation gff-to-bed [-hsV] [-o=<output>]
<gffFile>

Positional Input

This tool takes a single GFF file for input.

Output Options

Option	Description
-o, --output	specify output filename (default name will be same as original with .bed ext)
-s, --stdout	output bed to STDOUT
-z, --gzip	gzip output (default=false)