slopBed will increase the size of each feature in a feature file be a user-defined number of bases. While something like this could be done with an “awk ‘{OFS=”t” print $1,$2-<slop>,$3+<slop>}’”, slopBed will restrict the resizing to the size of the chromosome (i.e. no start < 0 and no end > chromosome size).
Usage:
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. |
By default, slopBed will either add a fixed number of bases in each direction (-b) or an asymmetric number of bases in each direction (-l and -r).
For example:
cat A.bed
chr1 5 100
chr1 800 980
cat my.genome
chr1 1000
slopBed -i A.bed -g my.genome -b 5
chr1 0 105
chr1 795 985
slopBed -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, slopBed will “clip” the feature accordingly.
cat A.bed
chr1 5 100
chr1 800 980
cat my.genome
chr1 1000
slopBed -i A.bed -g my.genome -b 5000
chr1 0 1000
chr1 0 1000
slopBed 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
slopBed -i A.bed -g my.genome -l 50 -r 80 -s
chr1 50 280 a1 1 +
chr1 20 250 a2 2 -