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: <URL: https://github.com/sanger-pathogens/snp-sites/tree/master/tests/data >

AUTHOR

snp-sites was originally written by Andrew Page (

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: <URL: 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.