.. _`samtools flagstat`:

Samtools flagstat
==========

Use samtools to create a flagstat file from a bam or sam file.


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


* samtools ==1.6


Example
-------

.. code-block:: bash

  rule samtools_flagstat:
    input:
      "mapped/{sample}.bam" # bam or sam file (.bam,.sam)
    output:
      "stat/{sample}.txt" # flagstat file (.flagstat)
    wrapper:
      "samtools/flagstat"


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/flagstat`` 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
-------


* Christopher Preusch