---
name: "bamcleanheader.py"
section: "1"
platform: "linux"
package: "bamkit"
version: "0.0.1+git20170413.ccd079d-3"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/bamcleanheader.py"
---

# bamcleanheader.py(1)

remove illegal and malformed fields from a BAM file's header

## NAME

bamcleanheader.py - remove illegal and malformed fields from a BAM file's header

## SYNOPSIS

**bamcleanheader.py** \[-h\] \[-S\] \[input \[input ...\]\]

## DESCRIPTION

remove illegal and malformed fields from a BAM file's header

## OPTIONS

### positional arguments:

- input

  SAM/BAM file to inject header lines into. If '-' or absent then defaults to stdin.

### optional arguments:

- **-h**, **--help**

  show this help message and exit

- **-S**, **--is\_sam**

  input is SAM

## AUTHOR

 This manpage was written by Andreas Tille for the Debian distribution and\
  can be used for any other usage of the program.