.. _`bio/gatk/variantstotable`:

GATK VARIANTSTOTABLE
====================


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

Run gatk VariantsToTable


**URL**: https://gatk.broadinstitute.org/hc/en-us/articles/360036896892-VariantsToTable

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule gatk_variantstotable:
        input:
            vcf="calls/snvs.vcf",
    #        intervals="intervals.bed",
        output:
            tab="calls/snvs.tab",
        log:
            "logs/gatk/varintstotable.log",
        params:
            extra="-F CHROM -F POS -F TYPE -GF AD",
            java_opts="",  # optional
        resources:
            mem_mb=1024,
        wrapper:
            "v3.0.1/bio/gatk/variantstotable"

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:**

* A VCF file to convert to a table

**Output:**

* A tab-delimited file containing the values of the requested fields in the VCF file




Authors
-------

* Dmitry Bespiatykh


Code
----

.. code-block:: python

    """Snakemake wrapper for GATK VariantsToTable"""

    __author__ = "Dmitry Bespiatykh"
    __copyright__ = "Copyright 2023, Dmitry Bespiatykh"
    __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)


    intervals = snakemake.input.get("intervals", "")
    if not intervals:
        intervals = snakemake.params.get("intervals", "")
    if intervals:
        intervals = "--intervals {}".format(intervals)


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


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