.. _`bio/jannovar`:

JANNOVAR
========


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

Annotate predicted effect of nucleotide changes with `Jannovar<https://doc-openbio.readthedocs.io/projects/jannovar/en/master/>`_


Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule jannovar:
        input:
            vcf="{sample}.vcf",
            pedigree="pedigree_ar.ped" # optional, contains familial relationships
        output:
            "jannovar/{sample}.vcf.gz"
        log:
            "logs/jannovar/{sample}.log"
        # optional specification of memory usage of the JVM that snakemake will respect with global
        # resource restrictions (https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#resources)
        # and which can be used to request RAM during cluster job submission as `{resources.mem_mg}`:
        # https://snakemake.readthedocs.io/en/latest/executing/cluster.html#job-properties
        resources:
            mem_mb = 1024,
        params:
            database="hg19_small.ser", # path to jannovar reference dataset
            extra="--show-all"         # optional parameters
        wrapper:
            "v3.0.1/bio/jannovar"

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
---------------------

* ``jannovar-cli=0.36``
* ``snakemake-wrapper-utils=0.6.2``




Authors
-------

* Bradford Powell


Code
----

.. code-block:: python

    __author__ = "Bradford Powell"
    __copyright__ = "Copyright 2018, Bradford Powell"
    __email__ = "bpow@unc.edu"
    __license__ = "BSD"


    from snakemake.shell import shell
    from snakemake_wrapper_utils.java import get_java_opts

    shell.executable("bash")

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

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

    pedigree = snakemake.input.get("pedigree", "")
    if pedigree:
        pedigree = '--pedigree-file "%s"' % pedigree

    shell(
        "jannovar annotate-vcf --database {snakemake.params.database}"
        " --input-vcf {snakemake.input.vcf} --output-vcf {snakemake.output}"
        " {pedigree} {extra} {java_opts} {log}"
    )


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