.. _`bio/varscan/somatic`:

VARSCAN SOMATIC
===============


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

`Varscan Somatic <http://varscan.sourceforge.net/somatic-calling.html>`_ calls variants and identifies their somatic status (Germline/LOH/Somatic) using pileup files from a matched tumor-normal pair.



Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule varscan_somatic:
        input:
            # A pair of pileup files can be used *instead* of the mpileup
            # normal_pileup = ""
            # tumor_pileup = ""
            mpileup = "mpileup/{sample}.mpileup.gz"
        output:
            snp = "vcf/{sample}.snp.vcf",
            indel = "vcf/{sample}.indel.vcf"
        message:
            "Calling somatic variants {wildcards.sample}"
        threads:
            1
        # 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_mb}`:
        # https://snakemake.readthedocs.io/en/latest/executing/cluster.html#job-properties
        resources:
            mem_mb=1024
        params:
            extra = ""
        wrapper:
            "v3.0.1/bio/varscan/somatic"

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

* ``varscan=2.4.6``
* ``snakemake-wrapper-utils=0.6.2``

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

* A pair of pileup files (Normal/Tumor)

**Output:**

* A VCF file




Authors
-------

* Thibault Dayris


Code
----

.. code-block:: python

    """Snakemake wrapper for varscan somatic"""

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


    import os.path as op

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

    # Defining logging and gathering extra parameters
    log = snakemake.log_fmt_shell(stdout=True, stderr=True)
    extra = snakemake.params.get("extra", "")
    java_opts = get_java_opts(snakemake)

    # Building output dirs
    makedirs(op.dirname(snakemake.output.snp))
    makedirs(op.dirname(snakemake.output.indel))

    # Output prefix
    prefix = op.splitext(snakemake.output.snp)[0]

    # Searching for input files
    pileup_pair = ["normal_pileup", "tumor_pileup"]

    in_pileup = ""
    mpileup = ""
    if "mpileup" in snakemake.input.keys():
        # Case there is a mpileup with both normal and tumor
        in_pileup = snakemake.input.mpileup
        mpileup = "--mpileup 1"
    elif all(pileup in snakemake.input.keys() for pileup in pileup_pair):
        # Case there are two separate pileup files
        in_pileup = " {snakemake.input.normal_pileup}" " {snakemakeinput.tumor_pileup} "
    else:
        raise KeyError("Could not find either a mpileup, or a pair of pileup files")

    shell(
        "varscan somatic"  # Tool and its subcommand
        " {in_pileup}"  # Path to input file(s)
        " {prefix}"  # Path to output
        " {java_opts} {extra}"  # Extra parameters
        " {mpileup}"
        " --output-snp {snakemake.output.snp}"  # Path to snp output file
        " --output-indel {snakemake.output.indel}"  # Path to indel output file
    )


.. |nl| raw:: html

   <br>