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

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 ([email protected])

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.