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
