.. _`bio/gatk/applybqsr`:

GATK APPLYBQSR
==============


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

Run gatk ApplyBQSR.


**URL**: https://gatk.broadinstitute.org/hc/en-us/articles/9570337264923-ApplyBQSR

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule gatk_applybqsr:
        input:
            bam="mapped/{sample}.bam",
            ref="genome.fasta",
            dict="genome.dict",
            recal_table="recal/{sample}.grp",
        output:
            bam="recal/{sample}.bam",
        log:
            "logs/gatk/gatk_applybqsr/{sample}.log",
        params:
            extra="",  # optional
            java_opts="",  # optional
            embed_ref=True,  # embed the reference in cram output
        resources:
            mem_mb=1024,
        wrapper:
            "v3.0.1/bio/gatk/applybqsr"

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 `java_opts` param allows for additional arguments to be passed to the java compiler, e.g. "-XX:ParallelGCThreads=10" (not for `-XmX` or `-Djava.io.tmpdir`, since they are handled automatically).
* The `extra` param allows for additional program arguments.


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

* ``gatk4=4.4.0.0``
* ``snakemake-wrapper-utils=0.6.2``
* ``samtools=1.18``

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

* BAM file
* FASTA reference
* recalibration table for the bam

**Output:**

* recalibrated bam file




Authors
-------

* Christopher Schröder
* Johannes Köster
* Jake VanCampen
* Filipe G. Vieira


Code
----

.. code-block:: python

    __author__ = "Christopher Schröder"
    __copyright__ = "Copyright 2020, Christopher Schröder"
    __email__ = "christopher.schroeder@tu-dortmund.de"
    __license__ = "MIT"


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

    # Extract arguments
    extra = snakemake.params.get("extra", "")
    reference = snakemake.input.get("ref")
    embed_ref = snakemake.params.get("embed_ref", False)
    java_opts = get_java_opts(snakemake)

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

    if snakemake.output.bam.endswith(".cram") and embed_ref:
        output = "/dev/stdout"
        pipe_cmd = " | samtools view -h -O cram,embed_ref -T {reference} -o {snakemake.output.bam} -"
    else:
        output = snakemake.output.bam
        pipe_cmd = ""

    with tempfile.TemporaryDirectory() as tmpdir:
        shell(
            "(gatk --java-options '{java_opts}' ApplyBQSR"
            " --input {snakemake.input.bam}"
            " --bqsr-recal-file {snakemake.input.recal_table}"
            " --reference {reference}"
            " {extra}"
            " --tmp-dir {tmpdir}"
            " --output {output}" + pipe_cmd + ") {log}"
        )


.. |nl| raw:: html

   <br>