############### 5.15 sortBed ############### **sortBed** sorts a feature file by chromosome and other criteria. ========================================================================== 5.15.1 Usage and option summary ========================================================================== Usage: :: sortBed [OPTIONS] -i =========================== =============================================================================================================================================================================================================== 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