.. _`samtools sort`:

Samtools sort
==========

Sort bam file with samtools.


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


* samtools ==1.6


Example
-------

.. code-block:: bash

  rule samtools_sort:
    input:
      "{sample}.bam" # A sam/bam/cram file
    output:
      "{sample}_sorted.bam" # A sorted sam/bam/cram file
    wrapper:
      "samtools/sort"


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/sort`` 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