complement


../../_images/complement-glyph.png

bedtools complement returns all intervals in a genome that are not covered by at least one interval in the input BED/GFF/VCF file.

See also

merge

Usage and option summary

Usage:

bedtools complement -i <BED/GFF/VCF> -g <GENOME>

(or):

complementBed -i <BED/GFF/VCF> -g <GENOME>

Default behavior

By default, bedtools complement returns all genomic intervals that are not covered by at least one record from the input file.

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

$ cat my.genome
chr1  1000
chr2  800

$ bedtools complement -i A.bed -g my.genome
chr1  0   100
chr1  200 400
chr1  800 1000
chr2  0   800
comments powered by Disqus