.. _`bedtools coverage`:

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
-------

.. code-block:: bash

  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

.. code-block:: bash

  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

.. code-block:: bash

    snakemake --use-conda

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




Authors
-------


* Jens Preußner