.. _`samtools view`:

Samtools view
==========

Convert or filter SAM/BAM.


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


* samtools ==1.6


Example
-------

.. code-block:: bash

  rule samtools_view:
    input:
      "{sample}.sam"
    output:
      "{sample}.bam"
    params:
      "-b"
    wrapper:
      "samtools/view"


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/view`` 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