'\" t
.\"     Title: snp-sites
.\"    Author: [see the "AUTHOR(S)" section]
.\" Generator: Asciidoctor 2.0.16
.\"      Date: 
.\"    Manual: \ \&
.\"    Source: \ \&
.\"  Language: English
.\"
.TH "SNP\-SITES" "1" "" "\ \&" "\ \&"
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.de URL
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.SH "NAME"
snp-sites \- finds SNP sites from a multi FASTA alignment file
.SH "SYNOPSIS"
.sp
snp\-sites [\-mvph] [\-o output_filename] [input file]
.SH "DESCRIPTION"
.sp
This application takes in a multi fasta alignment, finds all the SNP sites, then outputs the SNP sites in either of the following formats:
.sp
.RS 4
.ie n \{\
\h'-04'\(bu\h'+03'\c
.\}
.el \{\
.  sp -1
.  IP \(bu 2.3
.\}
multi fasta alignment
.RE
.sp
.RS 4
.ie n \{\
\h'-04'\(bu\h'+03'\c
.\}
.el \{\
.  sp -1
.  IP \(bu 2.3
.\}
VCF
.RE
.sp
.RS 4
.ie n \{\
\h'-04'\(bu\h'+03'\c
.\}
.el \{\
.  sp -1
.  IP \(bu 2.3
.\}
relaxed phylip format
.RE
.SH "OPTIONS"
.sp
\fB\-r\fP
.RS 4
Output internal pseudo reference sequence
.RE
.sp
\fB\-m\fP
.RS 4
Output a multi fasta alignment file (default)
.RE
.sp
\fB\-v\fP
.RS 4
Output a VCF file
.RE
.sp
\fB\-p\fP
.RS 4
Output a phylip file
.RE
.sp
\fB\-c\fP
.RS 4
Only output columns containing exclusively ACGT
.RE
.sp
\fB\-b\fP
.RS 4
Output monomorphic sites, useful for BEAST
.RE
.sp
\fB\-o\fP
.RS 4
Specify an output filename
.RE
.sp
\fB\-h\fP
.RS 4
Show help message
.RE
.sp
\fB\-V\fP
.RS 4
Show version and exit
.RE
.SH "EXAMPLES"
.sp
.if n .RS 4
.nf
.fam C
snp\-sites my\-alignment.aln
.fam
.fi
.if n .RE
.sp
.if n .RS 4
.nf
.fam C
snp\-sites my\-gzipped\-alignment.aln.gz
.fam
.fi
.if n .RE
.sp
.if n .RS 4
.nf
.fam C
snp\-sites \-cb \-o output_beast_format.aln inputfile.aln
.fam
.fi
.if n .RE
.SH "FORMAT OF THE INPUT FILE"
.sp
Input files should look like this:
.sp
.if n .RS 4
.nf
.fam C
>reference_sequence
aaccggtt
>comparison_sequence
AACCGGTT
>another_comparison_sequence
AACCGCTT
.fam
.fi
.if n .RE
.sp
For more examples, visit:
.URL "https://github.com/sanger\-pathogens/snp\-sites/tree/master/tests/data" "" ""
.SH "AUTHOR"
.sp
snp\-sites was originally written by Andrew Page (\c
.MTO "ap13\(atsanger.ac.uk" "" ")"
.SH "CITATION"
.sp
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: \c
.URL "http://dx.doi.org/10.1101/038190" "" ""
.SH "COPYING"
.sp
Wellcome Trust Sanger Institute Copyright \(co 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.