.. _`bio/gatk/mutect`:

GATK MUTECT2
============


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

Call somatic SNVs and indels via local assembly of haplotypes

**URL**: https://gatk.broadinstitute.org/hc/en-us/articles/360037593851-Mutect2

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule mutect2:
        input:
            fasta="genome/genome.fasta",
            map="mapped/{sample}.bam",
        output:
            vcf="variant/{sample}.vcf",
        message:
            "Testing Mutect2 with {wildcards.sample}"
        threads: 1
        resources:
            mem_mb=1024,
        log:
            "logs/mutect_{sample}.log",
        wrapper:
            "v3.0.1/bio/gatk/mutect"


    rule mutect2_bam:
        input:
            fasta="genome/genome.fasta",
            map="mapped/{sample}.bam",
        output:
            vcf="variant_bam/{sample}.vcf",
            bam="variant_bam/{sample}.bam",
        message:
            "Testing Mutect2 with {wildcards.sample}"
        threads: 1
        resources:
            mem_mb=1024,
        log:
            "logs/mutect_{sample}.log",
        wrapper:
            "v3.0.1/bio/gatk/mutect"


    rule mutect2_complete:
        input:
            fasta="genome/genome.fasta",
            map="mapped/{sample}.bam",
            intervals="genome/intervals.bed",
        output:
            vcf="variant_complete/{sample}.vcf",
            bam="variant_complete/{sample}.bam",
            f1r2="counts/{sample}.f1r2.tar.gz",
        message:
            "Testing Mutect2 with {wildcards.sample}"
        threads: 1
        resources:
            mem_mb=1024,
        log:
            "logs/mutect_{sample}.log",
        wrapper:
            "v3.0.1/bio/gatk/mutect"

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:**

* ``map``: Mapped reads (SAM/BAM/CRAM)
* ``fasta``: Reference Fasta file
* ``intervals``: Optional path to a BED interval file
* ``pon``: Optional path to Panel of Normals (flagged as BETA)
* ``germline``: Optional path to known germline variants

**Output:**

* ``vcf``: Path to variant file
* ``bam``: Optional path to output bam file
* ``f1r2``: Optional path to f1r2 count file



Params
------

* ``extra``: Optional parameters for GATK Mutect2

* ``use_parallelgc``: Automatically add "-XX:ParallelGCThreads={snakemake.threads}" to your command line. Set to `True`  if your architecture supports ParallelGCThreads.

* ``use_omp``: Automatically set `OMP_NUM_THREADS` environment variable. Set to `True` if your java architecture uses OMP threads.

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




Authors
-------

* Thibault Dayris
* Filipe G. Vieira


Code
----

.. code-block:: python

    """Snakemake wrapper for GATK4 Mutect2"""

    __author__ = "Thibault Dayris"
    __copyright__ = "Copyright 2019, Dayris Thibault"
    __email__ = "thibault.dayris@gustaveroussy.fr"
    __license__ = "MIT"

    import os
    import tempfile
    from snakemake.shell import shell
    from snakemake.utils import makedirs
    from snakemake_wrapper_utils.java import get_java_opts

    log = snakemake.log_fmt_shell(stdout=True, stderr=True)

    # On non-omp systems, and in case OMP_NUM_THREADS
    # was not set, define OMP_NUM_THREADS through python
    if "OMP_NUM_THREADS" not in os.environ.keys() and snakemake.params.get(
        "use_omp", False
    ):
        os.environ["OMP_NUM_THREADS"] = snakemake.threads


    bam_output = snakemake.output.get("bam", "")
    if bam_output:
        bam_output = f"--bam-output {bam_output }"


    germline_resource = snakemake.input.get("germline", "")
    if germline_resource:
        germline_resource = f"--germline-resource {germline_resource}"

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

    f1r2 = snakemake.output.get("f1r2", "")
    if f1r2:
        f1r2 = f"--f1r2-tar-gz {f1r2}"

    pon = snakemake.input.get("pon", "")
    if pon:
        pon = f"--panel-of-normals {pon}"

    extra = snakemake.params.get("extra", "")
    java_opts = get_java_opts(snakemake)

    # In case Java execution environment suits GC parallel
    # calls, these must be given as optional java parameters
    if snakemake.params.get("use_parallelgc", False):
        if "UseParallelGC" not in java_opts:
            java_opts += " -XX:+UseParallelGC "
        if "ParallelGCThreads" not in java_opts:
            java_opts += f" -XX:ParallelGCThreads={snakemake.threads}"


    with tempfile.TemporaryDirectory() as tmpdir:
        shell(
            "gatk --java-options '{java_opts}' Mutect2"  # Tool and its subprocess
            " --native-pair-hmm-threads {snakemake.threads}"
            " --input {snakemake.input.map}"  # Path to input mapping file
            " --reference {snakemake.input.fasta}"  # Path to reference fasta file
            " {f1r2}"  # Optional path to output f1r2 count file
            " {germline_resource}"  # Optional path to optional germline resource VCF
            " {intervals}"  # Optional path to optional bed intervals
            " {pon} "  # Optional path to panel of normals
            " {extra}"  # Extra parameters
            " --tmp-dir {tmpdir}"
            " --output {snakemake.output.vcf}"  # Path to output vcf file
            " {bam_output}"  # Path to output bam file, optional
            " {log}"  # Logging behaviour
        )


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