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
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