forked from samtools/samtools
-
Notifications
You must be signed in to change notification settings - Fork 0
/
samtools-markdup.1
110 lines (100 loc) · 2.81 KB
/
samtools-markdup.1
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
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
'\" t
.TH samtools-markdup 1 "14 August 2018" "samtools-1.9" "Bioinformatics tools"
.SH NAME
samtools markdup \- mark duplicate alignments in a coordinate sorted file
.\"
.\" Copyright (C) 2008-2011, 2013-2018 Genome Research Ltd.
.\" Portions copyright (C) 2010, 2011 Broad Institute.
.\"
.\" Author: Heng Li <[email protected]>
.\" Author: Joshua C. Randall <[email protected]>
.\"
.\" Permission is hereby granted, free of charge, to any person obtaining a
.\" copy of this software and associated documentation files (the "Software"),
.\" to deal in the Software without restriction, including without limitation
.\" the rights to use, copy, modify, merge, publish, distribute, sublicense,
.\" and/or sell copies of the Software, and to permit persons to whom the
.\" Software is furnished to do so, subject to the following conditions:
.\"
.\" The above copyright notice and this permission notice shall be included in
.\" all copies or substantial portions of the Software.
.\"
.\" THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
.\" IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
.\" FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
.\" THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
.\" LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
.\" FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
.\" DEALINGS IN THE SOFTWARE.
.
.\" For code blocks and examples (cf groff's Ultrix-specific man macros)
.de EX
. in +\\$1
. nf
. ft CR
..
.de EE
. ft
. fi
. in
..
.
.SH SYNOPSIS
.PP
samtools markdup
.RB [ -l
.IR length ]
.RB [ -r ]
.RB [ -s ]
.RB [ -T ]
.RB [ -S ]
.I in.algsort.bam out.bam
.SH DESCRIPTION
.PP
Mark duplicate alignments from a coordinate sorted file that
has been run through \fBsamtools fixmate\fR with the \fB-m\fR option. This program
relies on the MC and ms tags that fixmate provides.
.SH OPTIONS
.TP 11
.BI "-l " INT
.RI "Expected maximum read length of " INT " bases."
[300]
.TP
.B -r
Remove duplicate reads.
.TP
.B -s
Print some basic stats.
.TP
.BI "-T " PREFIX
Write temporary files to
.IB PREFIX . samtools . nnnn . mmmm . tmp
.TP
.B -S
Mark supplementary reads of duplicates as duplicates.
.SH EXAMPLES
This first command sort can be omitted if the file is already name ordered:
.EX
samtools sort -n -o namesort.bam example.bam
.EE
Add ms and MC tags for markdup to use later:
.EX
samtools fixmate -m namesort.bam fixmate.bam
.EE
Markdup needs position order:
.EX
samtools sort -o positionsort.bam fixmate.bam
.EE
Finally mark duplicates:
.EX
samtools markdup positionsort.bam markdup.bam
.EE
.SH AUTHOR
.PP
Written by Andrew Whitwham from the Sanger Institute.
.SH SEE ALSO
.IR samtools (1),
.IR samtools-sort (1),
.IR samtools-fixmate (1)
.PP
Samtools website: <http://www.htslib.org/>