---
name: "fastaq_insert_or_delete_bases"
section: "1"
platform: "linux"
package: "fastaq"
version: "1.5.0-1"
release: "Debian 8 (Jessie)"
platforms: ["linux"]
url: "https://new.carta.tech/fastaq_insert_or_delete_bases"
---

# fastaq\_insert\_or\_delete\_bases(1)

## NAME

fastaq\_insert\_or\_delete\_bases

## DESCRIPTION

 fastaq\_insert\_or\_delete\_bases \<fasta/q in\> \<outfile\>

Deletes or inserts bases at given position(s) from a fasta/q file

### positional arguments:

- infile

  Name of fasta/q file to be read

- outfile

  Name of output file

### optional arguments:

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

  show this help message and exit

- **-d** Name:start:bases, **--delete** Name:start:bases

  Delete the given bases from the given sequence. Format same as samtools view: name:start-end. This option can be used multiple times (once for each region to delete). Overlapping coords will be merged before deleting

- **--delete\_range** P,start,step

  Deletes bases starting at position P in each sequence of the input file. Deletes start + (n-1)\*step bases from sequence n.

- **-i** Name:start:bases, **--insert** Name:start:bases

  Insert a random string of bases at the given position. Format is name:position:number\_to\_add. Bases are added after the position. This option can be used multiple times

- **--insert\_range** P,start,step

  Inserts random bases starting after position P in each sequence of the input file. Inserts start + (n-1)\*step bases into sequence n.

## AUTHOR

fastaq\_insert\_or\_delete\_bases was originally written by Martin Hunt (mh12@sanger.ac.uk)

## COPYING

Wellcome Trust Sanger Institute Copyright © 2013 Wellcome Trust Sanger Institute This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version.