.. _`bio/gatk3/indelrealigner`:

GATK3 INDELREALIGNER
====================


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

Run gatk3 IndelRealigner



Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule indelrealigner:
        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",
            target_intervals="{sample}.intervals",
        output:
            bam="{sample}.realigned.bam",
            bai="{sample}.realigned.bai",
        log:
            "logs/gatk3/indelrealigner/{sample}.log",
        params:
            extra="--defaultBaseQualities 20 --filter_reads_with_N_cigar",  # optional
        threads: 16
        resources:
            mem_mb=1024,
        wrapper:
            "v4.6.0-24-g250dd3e/bio/gatk3/indelrealigner"

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" (memory is automatically inferred from `resources` and temp dir from `output.java_temp`.
* The `extra` param allows for additional program arguments.
* For more information see, https://github.com/broadinstitute/gatk-docs/blob/master/gatk3-tutorials/(howto)_Perform_local_realignment_around_indels.md
* 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=3.12.6``
* ``snakemake-wrapper-utils=0.6.2``

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

* bam file
* reference genome
* target intervals to realign
* bed file (optional)
* vcf files known variation (optional)

**Output:**

* indel realigned bam file
* indel realigned bai file (optional)
* temp dir (optional)




Authors
-------

* Patrik Smeds
* Filipe G. Vieira


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


    known = snakemake.input.get("known", "")
    if known:
        if isinstance(known, str):
            known = f"--knownAlleles {known}"
        else:
            known = list(map("----knownAlleles {}".format, known))


    output_bai = snakemake.output.get("bai", None)
    if output_bai is None:
        extra += " --disable_bam_indexing"


    shell(
        "gatk3 {java_opts}"
        " --analysis_type IndelRealigner"
        " --input_file {snakemake.input.bam}"
        " --reference_sequence {snakemake.input.ref}"
        " {known}"
        " {bed}"
        " --targetIntervals {snakemake.input.target_intervals}"
        " {extra}"
        " --out {snakemake.output.bam}"
        " {log}"
    )


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