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
