.. _`bio/gatk/applyvqsr`:

GATK APPLYVQSR
==============


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

Run gatk ApplyVQSR.


**URL**: https://gatk.broadinstitute.org/hc/en-us/articles/9570419503259-ApplyVQSR

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule apply_vqsr:
        input:
            vcf="test.vcf",
            recal="snps.recal",
            tranches="snps.tranches",
            ref="ref.fasta",
        output:
            vcf="test.snp_recal.vcf",
        log:
            "logs/gatk/applyvqsr.log",
        params:
            mode="SNP",  # set mode, must be either SNP, INDEL or BOTH
            extra="",  # optional
        resources:
            mem_mb=1024,
        wrapper:
            "v3.0.1/bio/gatk/applyvqsr"

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
* Recalibration file
* Tranches file

**Output:**

* Variant QualityScore-Recalibrated VCF




Authors
-------

* Brett Copeland
* Filipe G. Vieira


Code
----

.. code-block:: python

    __author__ = "Brett Copeland"
    __copyright__ = "Copyright 2021, Brett Copeland"
    __email__ = "brcopeland@ucsd.edu"
    __license__ = "MIT"


    import os
    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}' ApplyVQSR"
            " --variant {snakemake.input.vcf}"
            " --recal-file {snakemake.input.recal}"
            " --reference {snakemake.input.ref}"
            " --tranches-file {snakemake.input.tranches}"
            " --mode {snakemake.params.mode}"
            " {extra}"
            " --tmp-dir {tmpdir}"
            " --output {snakemake.output.vcf}"
            " {log}"
        )


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