5.1.9. 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

5.1.9.1. Usage and option summary¶

Usage:

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

(or):

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

5.1.9.2. 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

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Table Of Contents

5.1.9. complement
- 5.1.9.1. Usage and option summary
- 5.1.9.2. Default behavior

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