.. _`samtools mpileup`:

Samtools mpileup
==========

Generate VCF, BCF or pileup for BAM file(s).


Software dependencies
---------------------


* samtools >=1.6


Example
-------

.. code-block:: bash

  rule samtools_mpileup:
    input:
      "{sample}.bam" # One or many sam/bam/cram file(s)
    output:
      "{sample}.mpileup" # A pileup file
    params:
      options: "" # Additional command line options
    wrapper:
      "samtools/mpileup"


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 ``samtools/mpileup`` 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