.. _`bio/gatk/calculatecontamination`:

GATK CALCULATECONTAMINATION
===========================


.. image:: https://img.shields.io/github/issues-pr/snakemake/snakemake-wrappers/bio/gatk/calculatecontamination?label=version%20update%20pull%20requests
   :target: https://github.com/snakemake/snakemake-wrappers/pulls?q=is%3Apr+is%3Aopen+label%3Abio/gatk/calculatecontamination

Calculate the fraction of reads coming from cross-sample contamination


**URL**: https://gatk.broadinstitute.org/hc/en-us/articles/360036888972-CalculateContamination

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule test_gatk_calculate_contamination:
        input:
            tumor="pileups.table",
            # normal="normal.pileups.table",
        output:
            "contamination.table",
        threads: 1
        resources:
            mem_mb=1024,
        log:
            "logs/gatk/contamination.log",
        params:
            extra="",
        wrapper:
            "v3.0.1/bio/gatk/calculatecontamination"

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.


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

* ``gatk4=4.4.0.0``
* ``snakemake-wrapper-utils=0.6.2``

Input/Output
------------
**Input:**

* ``tumor``: Path to pileup table from GATK GetPileupSummaries
* ``normal``: Optional path to noram pileup table

**Output:**

* Path to contamination table



Params
------

* ``java_opts``: param allows for additional arguments to be passed to the java compiler, e.g. "-XX:ParallelGCThreads=10" (not for `-XmX` or `-Djava.io.tmpdir`, since they are handled automatically).

* ``extra``: param allows for additional program arguments.




Authors
-------

* Thibault Dayris


Code
----

.. code-block:: python

    __author__ = "Thibault Dayris"
    __copyright__ = "Copyright 2023, Thibault Dayris"
    __email__ = "thibault.dayris@gustaveroussy.fr"
    __license__ = "MIT"


    import tempfile
    from snakemake.shell import shell
    from snakemake_wrapper_utils.java import get_java_opts

    extra = snakemake.params.get("extra", "")
    java_opts = get_java_opts(snakemake)
    log = snakemake.log_fmt_shell(stdout=True, stderr=True)

    if snakemake.input.get("normal"):
        extra += f" --matched-normal {snakemake.input.normal}"

    with tempfile.TemporaryDirectory() as tmpdir:
        shell(
            "gatk --java-options '{java_opts}' CalculateContamination"
            " --input {snakemake.input.tumor}"
            " {extra}"
            " --tmp-dir {tmpdir}"
            " --output {snakemake.output}"
            " {log}"
        )


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