5.17 complementBed

complementBed returns the intervals in a genome that are not by the features in a feature file. An example usage of this tool would be to return the intervals of the genome that are not annotated as a repeat.

5.17.1 Usage and option summary

Usage:

complementBed [OPTIONS] -i <BED/GFF/VCF> -g <GENOME>

No additional options.

5.17.2 Default behavior

Figure:

Chromosome  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

BED FILE A     *************   ***************     ******************

Result      ===             ===               =====                  =======

For example:

cat A.bed
chr1  100  200
chr1  400  500
chr1  500  800

cat my.genome
chr1  1000

complementBed -i A.bed -g my.genome
chr1  0    100
chr1  200  400
chr1  800  1000