.. _`bio/gatk3/baserecalibrator`:

GATK3 BASERECALIBRATOR
======================


.. image:: https://img.shields.io/github/issues-pr/snakemake/snakemake-wrappers/bio/gatk3/baserecalibrator?label=version%20update%20pull%20requests
   :target: https://github.com/snakemake/snakemake-wrappers/pulls?q=is%3Apr+is%3Aopen+label%3Abio/gatk3/baserecalibrator

Run gatk3 BaseRecalibrator.



Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule baserecalibrator:
        input:
            bam="{sample}.bam",
            bai="{sample}.bai",
            ref="genome.fasta",
            fai="genome.fasta.fai",
            dict="genome.dict",
            known="dbsnp.vcf.gz",
            known_idx="dbsnp.vcf.gz.tbi",
        output:
            recal_table="{sample}.recal_data_table",
        log:
            "logs/gatk3/bqsr/{sample}.log",
        params:
            extra="--defaultBaseQualities 20 --filter_reads_with_N_cigar",  # optional
        resources:
            mem_mb=1024,
        threads: 16
        wrapper:
            "v3.0.1/bio/gatk3/baserecalibrator"

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. "-Xmx4G" for one, and "-Xmx4G -XX:ParallelGCThreads=10" for two options.
* The `extra` param allows for additional program arguments.
* For more information see, https://software.broadinstitute.org/gatk/documentation/article?id=11050
* Gatk3.jar is not included in the bioconda package, i.e it need to be added to the conda environment manually.


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

* ``gatk=3.8``
* ``python=3.12.0``
* ``snakemake-wrapper-utils=0.6.2``

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

* bam file
* vcf files
* reference genome

**Output:**

* recalibration table




Authors
-------

* Patrik Smeds


Code
----

.. code-block:: python

    __author__ = "Patrik Smeds"
    __copyright__ = "Copyright 2019, Patrik Smeds"
    __email__ = "patrik.smeds@gmail.com.com"
    __license__ = "MIT"

    import os

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

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


    bed = snakemake.params.get("bed", "")
    if bed:
        bed = f"--intervals {bed}"


    input_known = snakemake.input.get("known", "")
    if input_known:
        if isinstance(input_known, str):
            input_known = [input_known]
        input_known = list(map("--knownSites {}".format, input_known))


    shell(
        "gatk3 {java_opts}"
        " --analysis_type BaseRecalibrator"
        " --num_cpu_threads_per_data_thread {snakemake.threads}"
        " --input_file {snakemake.input.bam}"
        " {input_known}"
        " --reference_sequence {snakemake.input.ref}"
        " {bed}"
        " {extra}"
        " --out {snakemake.output}"
        " {log}"
    )


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