.. _`samtools merge`:

Samtools merge
==========

Merge two bam files with samtools.


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


* samtools ==1.6


Example
-------

.. code-block:: bash

  rule samtools_merge:
    input:
      list of bam files to merge
    output:
      merged bam file
    wrapper:
      "samtools/merge"


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/merge`` 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
-------


* Johannes Köster