.. _`bio/varscan/mpileup2snp`:

VARSCAN MPILEUP2SNP
===================


.. image:: https://img.shields.io/github/issues-pr/snakemake/snakemake-wrappers/bio/varscan/mpileup2snp?label=version%20update%20pull%20requests
   :target: https://github.com/snakemake/snakemake-wrappers/pulls?q=is%3Apr+is%3Aopen+label%3Abio/varscan/mpileup2snp

Detect variants in NGS data from Samtools mpileup with `VarScan <http://varscan.sourceforge.net/germline-calling.html>`_


Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule mpileup_to_vcf:
        input:
            "mpileup/{sample}.mpileup.gz"
        output:
            "vcf/{sample}.vcf"
        message:
            "Calling SNP with Varscan2"
        threads:  # Varscan does not take any threading information
            1     # However, mpileup might have to be unzipped.
                  # Keep threading value to one for unzipped mpileup input
                  # Set it to two for zipped mipileup files
        # 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
        log:
            "logs/varscan_{sample}.log"
        wrapper:
            "v3.0.1/bio/varscan/mpileup2snp"

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
-----

Varscan does not take any threading information by itself. However, mpileup
files given as input, might be gzipped.

If so, it's recommended to use two threads:

* 1 for varscan itself
* 1 for zcat


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

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

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

* A mpileup file

**Output:**

* A VCF file




Authors
-------

* Thibault Dayris


Code
----

.. code-block:: python

    """Snakemake wrapper for Varscan2 mpileup2snp"""

    __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

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

    # In case input files are gzipped mpileup files,
    # they are being unzipped and piped
    # In that case, it is recommended to use at least 2 threads:
    # - One for unzipping with zcat
    # - One for running varscan
    pileup = (
        " cat {} ".format(snakemake.input[0])
        if not snakemake.input[0].endswith("gz")
        else " zcat {} ".format(snakemake.input[0])
    )

    # Building output directories
    makedirs(op.dirname(snakemake.output[0]))

    shell(
        "varscan mpileup2snp "  # Tool and its subprocess
        "<( {pileup} ) "
        "{java_opts} {extra} "  # Extra parameters
        "> {snakemake.output[0]} "  # Path to vcf file
        "{log}"  # Logging behaviour
    )


.. |nl| raw:: html

   <br>