Category
Genomic Interval Manipulation
Usage
bedtools flank [OPTIONS] -i <BED/GFF/VCF> -g <GENOME> [-b or (-l and -r)]
Manual
This tool is part of the bedtools
suite and it's also known as flankBed
.
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). You may find bedtools slop
helpful, if you want to expand the entire regions.
Input regions: ====
Output regions: === ===
(-b 3
)
Output regions: ===
(-l 3
)
Output regions: ==== ====
(-b 1.0
-pct)
Required arguments
- -i <bed/gff/vcf>: Path to the input file (in bed/gff/vcf format) containing intervals to be manipulated.
- -g <genome>: Chromosome size file. The file should tab delimited and structured as follows: <chromName> <chromSize>. You can get this file for the genome release that you are working with by using
fetchChromSizes
.
- Flanking arguments: you must specify either the symmetric or asymmetric flanking arguments.
- Symmetric flanking:
- -b <integer>: Increase the BED/GFF/VCF entry by the same number base pairs in each direction.
- Asymmetric flanking: Both -l and -r parameters have to be specified.
- -l <integer>: The number of base pairs to subtract from the start coordinate.
- -r <integer>: The number of base pairs to add to the end coordinate.
Options
- -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 <float>: 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.
File formats this tool works with
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