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 © 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.

                                                                                     SNP-SITES(1)