.. _`bio/gatk/depthofcoverage`:

GATK DEPTHOFCOVERAGE
====================


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

Run gatk DepthOfCoverage (BETA).


**URL**: https://gatk.broadinstitute.org/hc/en-us/articles/9570475259291-DepthOfCoverage-BETA-

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule gatk_depth_of_coverage:
        input:
            bam="mapped/a.bam",  # File containing reads
            fasta="genome.fasta",
            intervals="regions.interval_list",  # Regions where the coverage is computed
        output:
            multiext(
                "depth/a",
                "",
                ".sample_interval_summary",
                ".sample_cumulative_coverage_counts",
                ".sample_cumulative_coverage_proportions",
                ".sample_interval_statistics",
                ".sample_statistics",
                ".sample_summary",
            ),
        log:
            "logs/gatk/depthofcoverage.log",
        params:
            extra="",
            java_opts="",
        resources:
            mem_mb=1024,
        wrapper:
            "v3.0.1/bio/gatk/depthofcoverage"

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 `extra` param allows for additional program arguments.


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

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

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

* one bam file to be analyzed for coverage statistics
* one or more genomic intervals over which to operate
* reference genome

**Output:**

* base file location to which to write coverage summary information




Authors
-------

* Lauri Mesilaakso


Code
----

.. code-block:: python

    __author__ = "Lauri Mesilaakso"
    __copyright__ = "Copyright 2022, Lauri Mesilaakso"
    __email__ = "lauri.mesilaakso@gmail.com"
    __license__ = "MIT"

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

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

    # Extract basename from the output file names
    out_basename = path.commonprefix(snakemake.output).rstrip(".")

    with tempfile.TemporaryDirectory() as tmpdir:
        shell(
            "gatk --java-options '{java_opts}' DepthOfCoverage"
            " --input {snakemake.input.bam}"
            " --intervals {snakemake.input.intervals}"
            " --reference {snakemake.input.fasta}"
            " --output {out_basename}"
            " --tmp-dir {tmpdir}"
            " {extra}"
            " {log}"
        )


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