---
name: "createChemistryHeader"
section: "1"
platform: "linux"
package: "pbalign"
version: "0.3.2-1"
release: "Debian 10 (Buster)"
platforms: ["linux"]
url: "https://new.carta.tech/createChemistryHeader"
---

# createChemistryHeader(1)

Create a SAM header with PacBio sequencing chemistry information

## NAME

createChemistryHeader - Create a SAM header with PacBio sequencing chemistry information

## DESCRIPTION

usage: getChemistryHeader.py \[-h\] \[--debug\] **--bas\_files** BAS\_FILES

- \[BAS\_FILES ...\]

  input\_alignment\_file output\_header\_file

createChemistryHeader creates a SAM header that contains the chemistry information used by Quiver.

### positional arguments:

- input\_alignment\_file

  A SAM or BAM file produced by BLASR.

- output\_header\_file

  Name of the SAM or BAM header file that will be created with chemistry information loaded.

### optional arguments:

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

  show this help message and exit

- **--debug**

  Output detailed log information. (default: False)

- **--bas\_files** BAS\_FILES \[BAS\_FILES ...\]

  The bas or bax files containing the reads that were aligned in the input\_alignment\_file. Also can be a fofn of bas or bax files. (default: None)

## AUTHOR

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