---
name: "bam2wig"
section: "1"
platform: "linux"
package: "augustus"
version: "3.5.0+dfsg-5"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/bam2wig"
---

# bam2wig(1)

Convert bam files to wiggle files. Can be used to generate exonpart hints for AUGUSTUS.

## NAME

bam2wig - Convert bam files to wiggle files. Can be used to generate exonpart hints for AUGUSTUS.

## SYNOPSIS

**bam2wig** \[-r region\] \[-t trackname\] \<in.bam\>

## OPTIONS

File needs to be sorted by Reference ID (i.e. target name) Use "samtools sort \<in.bam\>" to such effect. Use "samtools stats \<in.bam\> \| grep 'is sorted' " to check if the file is sorted.

### Parameters:

- **-r**

  Allows to specify a target region, e.g. 'chr3L:10-250' This option can only be used if an index file exists, see: samtools index

- **-t**

  string provided as track name

## AUTHORS

AUGUSTUS was written by M. Stanke, O. Keller, S. König, L. Gerischer and L. Romoth.

## ADDITIONAL DOCUMENTATION

An exhaustive documentation can be found in the file /usr/share/doc/augustus/README.md.gz.