.. _`bio/gatk/filtermutectcalls`:

GATK FILTERMUTECTCALLS
======================


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

Run gatk FilterMutectCalls to filter variants in a Mutect2 VCF callset.


**URL**: https://gatk.broadinstitute.org/hc/en-us/articles/9570331605531-FilterMutectCalls

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule gatk_filtermutectcalls:
        input:
            vcf="calls/snvs.vcf",
            ref="genome.fasta",
        output:
            vcf="calls/snvs.mutect.filtered.vcf",
        log:
            "logs/gatk/filter/snvs.log",
        params:
            extra="--max-alt-allele-count 3",  # optional arguments, see GATK docs
            java_opts="",  # optional
        resources:
            mem_mb=1024,
        wrapper:
            "v3.0.1/bio/gatk/filtermutectcalls"


    rule gatk_filtermutectcalls_complete:
        input:
            vcf="calls/snvs.vcf",
            ref="genome.fasta",
            bam="mapped/a.bam",
            intervals="intervals.bed",
            # contamination="", # from gatk CalculateContamination
            # segmentation="", # from gatk CalculateContamination
            # f1r2="", # from gatk LearnReadOrientationBias
        output:
            vcf="calls/snvs.mutect.filtered.b.vcf",
        log:
            "logs/gatk/filter/snvs.log",
        params:
            extra="--max-alt-allele-count 3",  # optional arguments, see GATK docs
            java_opts="",  # optional
        resources:
            mem_mb=1024,
        wrapper:
            "v3.0.1/bio/gatk/filtermutectcalls"

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.
* For more information see, https://software.broadinstitute.org/gatk/documentation/article?id=11050


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

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

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

* ``vcf``: Path to vcf file (pbgzipped, indexed)
* ``ref``: Path to reference genome (with .dict file alongside)
* ``aln``: Optional path to SAM/BAM/CRAM files
* ``contamination``: Optional path to
* ``segmentation``: Optional path to tumor segments
* ``f1r2``: Optional path to prior artefact (tar.gz2)
* ``intervels``: Optional file to BED intervals

**Output:**

* ``vcf``: filtered vcf file
* ``stats``: Optional stats from Mutect2




Authors
-------

* Patrik Smeds
* Filipe G. Vieira
* Thibault Dayris


Code
----

.. code-block:: python

    __author__ = "Patrik Smeds"
    __copyright__ = "Copyright 2021, Patrik Smeds"
    __email__ = "patrik.smeds@gmail.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)


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

    contamination = snakemake.input.get("contemination_table", "")
    if contamination:
        contamination = f"--contamination-table {contamination}"

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

    f1r2 = snakemake.input.get("f1r2", "")
    if f1r2:
        f1r2 = f"--orientation-bias-artifact-priors {f1r2}"

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

    with tempfile.TemporaryDirectory() as tmpdir:
        shell(
            "gatk --java-options '{java_opts}' FilterMutectCalls"
            " --variant {snakemake.input.vcf}"
            " --reference {snakemake.input.ref}"
            " {aln}"  # BAM/SAM/CRAM file containing reads
            " {contamination}"  # Tables containing contamination information
            " {segmentation}"  # Tumor segments' minor allele fractions
            " {f1r2}"  # .tar.gz files containing tables of prior artifact
            " {intervals}"  # Genomic intervals over which to operate
            " {extra}"
            " --tmp-dir {tmpdir}"
            " --output {snakemake.output.vcf}"
            " {log}"
        )


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