gtf2bed.rst

gtf2bed: convert GTF contents to BED format

Overview

gtf2bed converts the contents of a GTF file to BED format, printing a single line for each gene entry in the input GTF.

Usage

General usage syntax:

gtf2bed FILE.gtf

Output

The program prints the BED file contents directly to stdout, for example:

Gnai3   3   108107280   108146146   -   gene
Pbsn    X   77837901    77853623    -   gene
Cdc45   16  18780447    18811987    -   gene
H19 7   142575529   142578143   -   gene
Scml2   X   161117193   161258213   +   gene

To sent this to a file use:

gtf2bed FILE.gtf > FILE.bed

If any problems are encountered then the program will print warning messages to stderr.