---
name: "convert2bed"
section: "1"
platform: "linux"
package: "bedops"
version: "2.4.41+dfsg-3"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/convert2bed"
---

# convert2bed(1)

manual page for convert2bed 2.4.41+dfsg

## NAME

convert2bed - manual page for convert2bed 2.4.41+dfsg

## DESCRIPTION

convert2bed

- version:

  2\.4.41

- author:

  Alex Reynolds

-

  Usage:

-

  `$ convert2bed --input=fmt [--output=fmt] [options] < input > output`

-

  Convert BAM, GFF, GTF, GVF, PSL, RepeatMasker (OUT), SAM, VCF and WIG genomic formats to BED or BEDOPS Starch (compressed BED)

-

  Input can be a regular file or standard input piped in using the hyphen character ('-'):

-

  `$ some_upstream_process ... | convert2bed --input=fmt - > output`

-

  Input (required):

**--input**=*\[bam*\|gff\|gtf\|gvf\|psl\|rmsk\|sam\|vcf\|wig\] (**-i** \<fmt\>)

-

  Genomic format of input file (required)

-

  Output:

**--output**=*\[bed*\|starch\] (**-o** \<fmt\>)

-

  Format of output file, either BED or BEDOPS Starch (optional, default is BED)

-

  Other processing options:

**--do-not-sort** (**-d**)

-

  Do not sort BED output with sort-bed (not compatible with **--output**=*starch*)

**--max-mem=**\<value\> (**-m** \<val\>)

-

  Sets aside \<value\> memory for sorting BED output. For example, \<value\> can be 8G, 8000M or 8000000000 to specify 8 GB of memory (default is 2G)

**--sort-tmpdir=**\<dir\> (**-r** \<dir\>)

-

  Optionally sets \[dir\] as temporary directory for sort data, when used in conjunction with **--max-mem**=*\[value\]*, instead of the host's operating system default temporary directory

**--starch-bzip2** (**-z**)

-

  Used with **--output**=*starch*, the compressed output explicitly applies the bzip2 algorithm to compress intermediate data (default is bzip2)

**--starch-gzip** (**-g**)

-

  Used with **--output**=*starch*, the compressed output applies gzip compression on intermediate data

**--starch-note=**"xyz..." (**-e** "xyz...")

-

  Used with **--output**=*starch*, this adds a note to the Starch archive metadata

**--help** \| **--help\[-bam**\|-gff\|-gtf\|-gvf\|-psl\|-rmsk\|-sam\|-vcf\|-wig\] (**-h** \| **-h** \<fmt\>)

-

  Show general help message (or detailed help for a specified input format)

**--version** (**-w**)

-

  Show application version

## SEE ALSO

The full documentation for **convert2bed** is maintained as a Texinfo manual.  If the **info** and **convert2bed** programs are properly installed at your site, the command

-

  **info convert2bed**

should give you access to the complete manual.