SNP-SITES(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:

 - multi fasta alignment
 - VCF
 - relaxed phylip format

OPTIONS
-------
*-r*::
	Output internal pseudo reference sequence

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

*-v*::
	Output a VCF file

*-p*::
	Output a phylip file

*-c*::
	Only output columns containing exclusively ACGT

*-b*::
	Output monomorphic sites, useful for BEAST

*-o*::
	Specify an output filename

*-h*::
	Show help message

*-V*::
	Show version and exit


EXAMPLES
--------

 snp-sites my-alignment.aln

 snp-sites my-gzipped-alignment.aln.gz
 
 snp-sites -cb -o output_beast_format.aln inputfile.aln


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)

CITATION
--------
If you use this program, please cite:
"SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments",
Andrew J. Page, Ben Taylor, Aidan J. Delaney, Jorge Soares, Torsten Seemann, Jacqueline A. Keane, Simon R. Harris (2016),
bioRxiv doi: http://dx.doi.org/10.1101/038190

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.
