slop — bedtools 2.31.0 documentation

# slop

`bedtools slop` will increase the size of each feature in a feature file by a user-defined number of bases. While something like this could be done with an `awk '{OFS="\t" print $1,$2-<slop>,$3+<slop>}'`, `bedtools slop` will restrict the resizing to the size of the chromosome (i.e. no start < 0 and no end > chromosome size).

Note

In order to prevent the extension of intervals beyond chromosome boundaries, `bedtools slop` requires a genome file defining the length of each chromosome or contig.

See also

flank

## Usage and option summary

Usage:

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

(or):

    slopBed [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.
-header | Print the header from the input file prior to results.

## Default behavior

By default, `bedtools slop` 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 5 100
    chr1 800 980

    $ cat my.genome
    chr1 1000

    $ bedtools slop -i A.bed -g my.genome -b 5
    chr1 0 105
    chr1 795 985

    $ bedtools slop -i A.bed -g my.genome -l 2 -r 3
    chr1 3 103
    chr1 798 983

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

    $ cat A.bed
    chr1  5   100
    chr1  800 980

    $ cat my.genome
    chr1  1000

    $ bedtools slop -i A.bed -g my.genome -b 5000
    chr1  0   1000
    chr1  0   1000

## `-s` Resizing features according to strand

`bedtools slop` will optionally increase the size of a feature based on strand.

For example:

    $ cat A.bed
    chr1 100 200 a1 1 +
    chr1 100 200 a2 2 -

    $ cat my.genome
    chr1 1000

    $ bedtools slop  -i A.bed -g my.genome -l 50 -r 80 -s
    chr1 50  280 a1 1 +
    chr1 20  250 a2 2 -

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

`bedtools slop` will optionally increase the size of a feature by a user-specific fraction.

For example:

    $ cat A.bed
    chr1 100 200 a1 1 +

    $ bedtools slop -i A.bed -g my.genome -b 0.5 -pct
    chr1 50  250 a1 1 +

    $ bedtools slop -i a.bed -l 0.5 -r 0.0 -pct -g my.genome
    chr1  50      200     a1      1       +

## `-header` Print the header for the A file before reporting results.

By default, if your A file has a header, it is ignored when reporting results. This option will instead tell bedtools to first print the header for the A file prior to reporting results.

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