Finds snp sites from a multi fasta alignment file
snp_sites [-mvph] [-o output_filename] [input file]
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.
-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
snp-sites my-alignment.aln
snp-sites my-gzipped-alignment.aln.gz
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
snp-sites was originally written by Andrew Page ([email protected])
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.