.. _`bio/gatk/selectvariants`:

GATK SELECTVARIANTS
===================


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   :target: https://github.com/snakemake/snakemake-wrappers/pulls?q=is%3Apr+is%3Aopen+label%3Abio/gatk/selectvariants

Run gatk SelectVariants.


**URL**: https://gatk.broadinstitute.org/hc/en-us/articles/9570332289307-SelectVariants

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule gatk_select:
        input:
            vcf="calls/all.vcf",
            ref="genome.fasta",
        output:
            vcf="calls/snvs.vcf",
        log:
            "logs/gatk/select/snvs.log",
        params:
            extra="--select-type-to-include SNP",  # optional filter arguments, see GATK docs
            java_opts="",  # optional
        resources:
            mem_mb=1024,
        wrapper:
            "v3.0.1/bio/gatk/selectvariants"

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.


Notes
-----

* The `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).
* The `extra` param allows for additional program arguments.


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

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

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

* vcf file
* reference genome

**Output:**

* filtered vcf file




Authors
-------

* Johannes Köster
* Jake VanCampen
* Filipe G. Vieira


Code
----

.. code-block:: python

    __author__ = "Johannes Köster"
    __copyright__ = "Copyright 2018, Johannes Köster"
    __email__ = "johannes.koester@protonmail.com"
    __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)

    with tempfile.TemporaryDirectory() as tmpdir:
        shell(
            "gatk --java-options '{java_opts}' SelectVariants"
            " --variant {snakemake.input.vcf}"
            " --reference {snakemake.input.ref}"
            " {extra}"
            " --tmp-dir {tmpdir}"
            " --output {snakemake.output.vcf}"
            " {log}"
        )


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