flank — bedtools 2.31.0 documentation

# flank

`bedtools flank` will create two new flanking intervals for each interval in a BED/GFF/VCF file. Note that `flank` will restrict the created flanking intervals to the size of the chromosome (i.e. no start < 0 and no end > chromosome size).

Note

In order to prevent creating intervals that violate chromosome boundaries, `bedtools flank` requires a genome file defining the length of each chromosome or contig.

See also

slop

## Usage and option summary

Usage:

    bedtools flank [OPTIONS] -i <BED/GFF/VCF> -g <GENOME> [-b or (-l and -r)]

(or):

    flankBed [OPTIONS] -i <BED/GFF/VCF> -g <GENOME> [-b or (-l and -r)]

Option | Description
--- | ---
-b | Increase the BED/GFF/VCF entry by the same number base pairs in each direction. Integer.
-l | The number of base pairs to subtract from the start coordinate. Integer.
-r | The number of base pairs to add to the end coordinate. Integer.
-s | Define -l and -r based on strand. For example. if used, -l 500 for a negative-stranded feature, it will add 500 bp to the end coordinate.
-pct | Define -l and -r as a fraction of the feature’s length. E.g. if used on a 1000bp feature, -l 0.50, will add 500 bp “upstream”. Default = false.

## Default behavior

By default, `bedtools flank` will either add a fixed number of bases in each direction (`-b`) or an asymmetric number of bases in each direction with `-l` and `-r`.

    $ cat A.bed
    chr1 100 200
    chr1 500 600

    $ cat my.genome
    chr1 1000

    $ bedtools flank -i A.bed -g my.genome -b 5
    chr1  95      100
    chr1  200     205
    chr1  495     500
    chr1  600     605

    $ bedtools flank -i A.bed -g my.genome -l 2 -r 3
    chr1  98      100
    chr1  200     203
    chr1  498     500
    chr1  600     603

However, if the requested number of bases exceeds the boundaries of the chromosome, `bedtools flank` will “clip” the feature accordingly.

    $ cat A.bed
    chr1 100 200
    chr1 500 600

    $ cat my.genome
    chr1 1000

    $ bedtools flank -i A.bed -g my.genome -b 800
    chr1  0       100
    chr1  200     1000
    chr1  0       500
    chr1  600     1000

## `-pct` Resizing features by a given fraction

`bedtools flank` will optionally create flanking intervals whose size is user-specified fraction of the original interval.

For example:

    $ cat A.bed
    chr1 100 200
    chr1 500 700

    ################################################################
    # note the flanking intervals from the second record in A.bed
    # are 20bp whereas the flanking intervals from the first record
    # are only 10bp
    ################################################################
    $ bedtools flank -i A.bed -g my.genome -b 0.1 -pct
    chr1  90      100
    chr1  200     210
    chr1  480     500
    chr1  700     720

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