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.. _sort:
###############
*sort*
###############
**sortBed** sorts a feature file by chromosome and other criteria.
==========================================================================
Usage and option summary
==========================================================================
Usage:
::
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, then by feature size (asc).
**-chrThenSizeD** Sort by chromosome, then by feature size (desc).
**-chrThenScoreA** Sort by chromosome, then by score (asc).
**-chrThenScoreD** Sort by chromosome, then by score (desc).
=========================== ===============================================================================================================================================================================================================
==========================================================================
Default behavior
==========================================================================
By default, **sortBed** 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
==========================================================================
**sortBed** will also sorts 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 **sortBed** 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
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