.. _`bio/gatk/getpileupsummaries`:

GATK GETPILEUPSUMMARIES
=======================


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

Summarizes counts of reads that support reference, alternate and other alleles

**URL**: https://gatk.broadinstitute.org/hc/en-us/articles/9570416554907-GetPileupSummaries

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule test_gatk_get_pileup_summaries:
        input:
            bam="mapped/a.bam",
            intervals="genome/intervals.bed",
            variants="genome/variants.vcf.gz",
        output:
            "summaries.table",
        threads: 1
        resources:
            mem_mb=1024,
        params:
            extra="",
        log:
            "logs/summary.log",
        wrapper:
            "v3.0.1/bio/gatk/getpileupsummaries"

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

* ``gatk4=4.4.0.0``
* ``snakemake-wrapper-utils=0.6.2``

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

* ``bam``: Path to bam file (sorted and indexed)
* ``intervals``: Path to one or more BED genomic intervals over which to operate
* ``variants``: Path to a VCF containing allele frequencies (pbgzipped and tabix indexed)

**Output:**

* Path to output table



Params
------

* ``extra``: Optional parameters




Authors
-------



Code
----

.. code-block:: python

    #!/usr/bin/env python3
    # coding: utf-8

    """Snakemake wrapper for GATK GetPileupSummaries"""

    __author__ = "Thibault Dayris"
    __copyright__ = "Copyright 2022, Thibault Dayris"
    __email__ = "thibault.dayris@gustaveroussy.fr"
    __license__ = "MIT"


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

    log = snakemake.log_fmt_shell(stdout=True, stderr=True)
    extra = snakemake.params.get("extra", "")
    java_opts = get_java_opts(snakemake)

    with tempfile.TemporaryDirectory() as tempdir:
        shell(
            "gatk GetPileupSummaries "
            "--java-options '{java_opts}' "
            "--input {snakemake.input.bam} "
            "--intervals {snakemake.input.intervals} "
            "--variant {snakemake.input.variants} "
            "--output {snakemake.output[0]} "
            "--tmp-dir {tempdir} "
            "{extra} "
            "{log} "
        )


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