Bedtools makewindows

Makes adjacent or sliding windows across a genome or BED file.

Software dependencies

• bedtools >=2.27.1

Example

rule bedtools_makewindows:
  input:
    bed = "{sample}.bed" # The path to a bed file. Windows will be created for each interval in the file.
    genome = "genome.sizes" # The path to the genome size file. Windows will be created for each chromosome in the file.
  output:
    "extended.bed"
  params:
    options = "" # Additional command line options
  wrapper:
    "bedtools/makewindows"

Usage

Run snakemake with

snakemake --wrapper-prefix https://github.molgen.mpg.de/raw/loosolab/snakemake-wrappers/master/

to automatically download the wrapper bedtools/makewindows and include it in the snakefile.

Note that input, output and log file paths can be chosen freely. When running with

snakemake --use-conda

the software dependencies will be automatically deployed into an isolated environment before execution.

Authors

• Jens Preußner