complement

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

-L Only report chromosomes that are in the -i file

Use the "-L" option to L`imit the output to solely the chromosomes that are represented in the `-i file. Chromosomes that are in -g but not -i will be suppressed

For example (note the difference in coverage with and without -s:

$ 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

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