# 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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