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