Bedtools coverage

Computes both the depth and breadth of coverage of features in file B on the features in file A.

Software dependencies

• bedtools >=2.27.1

Example

rule bedtools_coverage:
  input:
    "peaks/peaks.bed" # A bam/bed/gff/vcf file A. Each feature in A is compared to B in search of overlaps.
    "mapped/{sample}.bam" # A bam/bed/gff/vcf file B.
  output:
    "counts/{sample}.bed" # A bed file.
  params:
    options = "" # Additional command line options
  wrapper:
    "bedtools/coverage"

Usage

Run snakemake with

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

to automatically download the wrapper bedtools/coverage 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