5.15 sortBed

sortBed sorts a feature file by chromosome and other criteria.

5.15.1 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).

5.15.2 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

5.15.3 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 -k2,2 -n a.bed
chr1 1   10
chr1 80  180
chr1 750 10000
chr1 800 1000