slop


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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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