.. _`bio/gatk/genotypegvcfs`:

GATK GENOTYPEGVCFS
==================


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

Run gatk GenotypeGVCFs.


**URL**: https://gatk.broadinstitute.org/hc/en-us/articles/9570489472411-GenotypeGVCFs

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule genotype_gvcfs:
        input:
            gvcf="calls/all.g.vcf",  # combined gvcf over multiple samples
    	# N.B. gvcf or genomicsdb must be specified
    	# in the latter case, this is a GenomicsDB data store
            ref="genome.fasta"
        output:
            vcf="calls/all.vcf",
        log:
            "logs/gatk/genotypegvcfs.log"
        params:
            extra="",  # optional
            java_opts="", # optional
        resources:
            mem_mb=1024
        wrapper:
            "v3.0.1/bio/gatk/genotypegvcfs"

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:**

* GVCF files or GenomicsDB workspace
* reference genome

**Output:**

* VCF file with genotypes




Authors
-------

* Johannes Köster
* Jake VanCampen
* Filipe G. Vieira


Code
----

.. code-block:: python

    __author__ = "Johannes Köster"
    __copyright__ = "Copyright 2018, Johannes Köster"
    __email__ = "johannes.koester@protonmail.com"
    __license__ = "MIT"


    import os
    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)

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

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

    # Allow for either an input gvcf or GenomicsDB
    gvcf = snakemake.input.get("gvcf", "")
    genomicsdb = snakemake.input.get("genomicsdb", "")
    if gvcf:
        if genomicsdb:
            raise Exception("Only input.gvcf or input.genomicsdb expected, got both.")
        input_string = gvcf
    else:
        if genomicsdb:
            input_string = "gendb://{}".format(genomicsdb)
        else:
            raise Exception("Expected input.gvcf or input.genomicsdb.")

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


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


.. |nl| raw:: html

   <br>