SNP-SITESDOC(1)
==============
:doctype: manpage


NAME
----
snp-sites - finds snp sites from a multi fasta alignment file

SYNOPSIS
--------
snp_sites [-mvph] [-o output_filename] [input file]

DESCRIPTION
-----------
This application takes in a multi fasta alignment, finds all the SNP sites, then outputs the SNP sites in either of the following formats:

a multi fasta alignment, VCF, relaxed phylip format.

OPTIONS
-------
*-m*::
	Output a multi fasta alignment file (default)

*-v*::
	Output a VCF file

*-p*::
	Output a phylip file

*-o*::
	Specify an output filename

*-h*::
	This document

*-V*::
	Show version and exit

EXAMPLES
--------
snp-sites my-alignment.aln

snp-sites my-gzipped-alignment.aln.gz


FORMAT OF THE INPUT FILE
------------------------

Input files should look like this:

>reference_sequence
aaccggtt
>comparison_sequence
AACCGGTT
>another_comparison_sequence
AACCGCTT

For more examples, visit:
https://github.com/sanger-pathogens/snp_sites/tree/master/tests/data

AUTHOR
------
snp-sites was originally written by Andrew Page (ap13@sanger.ac.uk)

COPYING
-------
Wellcome Trust Sanger Institute Copyright (C) 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.