.. _`bio/gatk/varianteval`:

GATK VARIANTEVAL
================


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

Run gatk VariantEval.


**URL**: https://gatk.broadinstitute.org/hc/en-us/articles/9570243836187-VariantEval-BETA-

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule gatk_varianteval:
        input:
            vcf="calls/snvs.vcf",
            ref="genome.fasta",
            dict="genome.dict",
            # comp="calls/comp.vcf", # optional comparison VCF
        output:
            vcf="snvs.varianteval.grp",
        log:
            "logs/gatk/varianteval/snvs.log",
        params:
            extra="",  # optional arguments, see GATK docs
            java_opts="",  # optional
        resources:
            mem_mb=1024,
        wrapper:
            "v3.0.1/bio/gatk/varianteval"

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 files
* BAM/CRAM files (optional)
* reference genome (optional)
* reference dictionary (optional)
* vcf.gz of known variants (optional)
* PED (pedigree) file (optional)

**Output:**

* Evaluation tables detailing the results of the eval modules on VCF file




Authors
-------

* Filipe G. Vieira


Code
----

.. code-block:: python

    __author__ = "Filipe G. Vieira"
    __copyright__ = "Copyright 2021, 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)


    vcf = snakemake.input.vcf
    if isinstance(vcf, str):
        vcf = "--eval  {}".format(vcf)
    else:
        vcf = list(map("--eval {}".format, vcf))

    bam = snakemake.input.get("bam", "")
    if bam:
        if isinstance(bam, str):
            bam = "--input  {}".format(bam)
        else:
            bam = list(map("--input {}".format, bam))

    ref = snakemake.input.get("ref", "")
    if ref:
        ref = "--reference " + ref

    ref_dict = snakemake.input.get("dict", "")
    if ref_dict:
        ref_dict = "--sequence-dictionary " + ref_dict

    known = snakemake.input.get("known", "")
    if known:
        known = "--dbsnp " + known

    comp = snakemake.input.get("comp", "")
    if comp:
        if isinstance(comp, str):
            comp = "--comparison  {}".format(comp)
        else:
            comp = list(map("--comparison {}".format, comp))

    ped = snakemake.input.get("ped", "")
    if ped:
        ped = "--pedigree " + ped


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


    with tempfile.TemporaryDirectory() as tmpdir:
        shell(
            "gatk --java-options '{java_opts}' VariantEval"
            " {vcf}"
            " {bam}"
            " {ref}"
            " {ref_dict}"
            " {known}"
            " {ped}"
            " {comp}"
            " {extra}"
            " --tmp-dir {tmpdir}"
            " --output {snakemake.output[0]}"
            " {log}"
        )


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