forked from sanger-pathogens/snp-sites
-
Notifications
You must be signed in to change notification settings - Fork 0
/
snp-sites.txt
91 lines (64 loc) · 1.92 KB
/
snp-sites.txt
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
SNP-SITES(1)
============
:doctype: manpage
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 ([email protected])
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 (C) 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.