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
|
.. _sort:
###############
*sort*
###############
The ``bedtools sort`` tool sorts a feature file by chromosome and other criteria.
==========================================================================
Usage and option summary
==========================================================================
**Usage**:
::
bedtools sort [OPTIONS] -i <BED/GFF/VCF>
**(or)**:
::
sortBed [OPTIONS] -i <BED/GFF/VCF>
=========================== ===============================================================================================================================================================================================================
Option Description
=========================== ===============================================================================================================================================================================================================
**-sizeA** Sort by feature size in ascending order.
**-sizeD** Sort by feature size in descending order.
**-chrThenSizeA** Sort by chromosome (asc), then by feature size (asc).
**-chrThenSizeD** Sort by chromosome (asc), then by feature size (desc).
**-chrThenScoreA** Sort by chromosome (asc), then by score (asc).
**-chrThenScoreD** Sort by chromosome (asc), then by score (desc).
**-g** Define sort order by order of tab-delimited file with chromosome names in the first column.
**-faidx** Define sort order by order of tab-delimited file with chromosome names in the first column. Sort by specified chromosome order.
=========================== ===============================================================================================================================================================================================================
==========================================================================
Default behavior
==========================================================================
By default, ``bedtools sort`` sorts a BED file by chromosome and then by start position in ascending order.
For example:
::
cat A.bed
chr1 800 1000
chr1 80 180
chr1 1 10
chr1 750 10000
sortBed -i A.bed
chr1 1 10
chr1 80 180
chr1 750 10000
chr1 800 1000
==========================================================================
Optional sorting behavior
==========================================================================
``bedtools sort`` will also sort a BED file by chromosome and then by other criteria.
For example, to sort by chromosome and then by feature size (in descending order):
::
cat A.bed
chr1 800 1000
chr1 80 180
chr1 1 10
chr1 750 10000
sortBed -i A.bed -sizeD
chr1 750 10000
chr1 800 1000
chr1 80 180
chr1 1 10
**Disclaimer:** it should be noted that ``bedtools sort`` is merely a convenience utility, as the UNIX sort utility
will sort BED files more quickly while using less memory. For example, UNIX sort will sort a BED file
by chromosome then by start position in the following manner:
::
sort -k 1,1 -k2,2n a.bed
chr1 1 10
chr1 80 180
chr1 750 10000
chr1 800 1000
|
