.. _`bio/gatk/variantannotator`:

GATK VARIANTANNOTATOR
=====================


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

Run gatk VariantAnnotator.


**URL**: https://gatk.broadinstitute.org/hc/en-us/articles/9570271608219-VariantAnnotator

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule gatk_annotator:
        input:
            vcf="calls/snvs.vcf.gz",
            aln="mapped/a.bam",
            bai="mapped/a.bam.bai",
            ref="genome.fasta",
            db="calls/snvs.vcf.gz",
    #        intervals="targets.bed",
        output:
            vcf="snvs.annot.vcf",
        log:
            "logs/gatk/annotator/snvs.log",
        params:
            extra="--resource-allele-concordance -A Coverage --expression db.END",
            java_opts="",  # optional
        resources:
            mem_mb=1024,
        wrapper:
            "v3.0.1/bio/gatk/variantannotator"

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
* BAM file
* reference genome
* VCF of known variation

**Output:**

* annotated VCF file




Authors
-------

* Filipe G. Vieira


Code
----

.. code-block:: python

    __author__ = "Filipe G. Vieira"
    __copyright__ = "Copyright 2022, Filipe G. Vieira"
    __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)


    input = snakemake.input.get("aln", "")
    if input:
        input = f"--input {input}"

    reference = snakemake.input.get("ref", "")
    if reference:
        reference = f"--reference {reference}"

    dbsnp = snakemake.input.get("known", "")
    if dbsnp:
        dbsnp = f"--dbsnp {dbsnp}"

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

    resources = [
        f"--resource:{name} {file}"
        for name, file in snakemake.input.items()
        if name not in ["vcf", "aln", "ref", "known", "intervals", "bai"]
    ]


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


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