.. _`bio/gatk/haplotypecaller`:

GATK HAPLOTYPECALLER
====================


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

Run gatk HaplotypeCaller.


**URL**: https://gatk.broadinstitute.org/hc/en-us/articles/9570334998171-HaplotypeCaller

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule haplotype_caller:
        input:
            # single or list of bam files
            bam="mapped/{sample}.bam",
            ref="genome.fasta",
            # known="dbsnp.vcf"  # optional
        output:
            vcf="calls/{sample}.vcf",
        # 	bam="{sample}.assemb_haplo.bam",
        log:
            "logs/gatk/haplotypecaller/{sample}.log",
        params:
            extra="",  # optional
            java_opts="",  # optional
        threads: 4
        resources:
            mem_mb=1024,
        wrapper:
            "v3.0.1/bio/gatk/haplotypecaller"

    rule haplotype_caller_gvcf:
        input:
            # single or list of bam files
            bam="mapped/{sample}.bam",
            ref="genome.fasta",
            # known="dbsnp.vcf"  # optional
        output:
            gvcf="calls/{sample}.g.vcf",
        # 	bam="{sample}.assemb_haplo.bam",
        log:
            "logs/gatk/haplotypecaller/{sample}.log",
        params:
            extra="",  # optional
            java_opts="",  # optional
        threads: 4
        resources:
            mem_mb=1024,
        wrapper:
            "v3.0.1/bio/gatk/haplotypecaller"

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``

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

* BAM file

**Output:**

* GVCF file




Authors
-------

* Johannes Köster
* Jake VanCampen
* Filipe G. Vieira


Code
----

.. code-block:: python

    __author__ = "Johannes Köster"
    __copyright__ = "Copyright 2018, Johannes Köster"
    __email__ = "johannes.koester@protonmail.com"
    __license__ = "MIT"


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

    extra = snakemake.params.get("extra", "")
    java_opts = get_java_opts(snakemake)

    bams = snakemake.input.bam
    if isinstance(bams, str):
        bams = [bams]
    bams = list(map("--input {}".format, bams))

    intervals = snakemake.input.get("intervals", "")
    if not intervals:
        intervals = snakemake.params.get("intervals", "")
    if intervals:
        intervals = "--intervals {}".format(intervals)

    known = snakemake.input.get("known", "")
    if known:
        known = "--dbsnp " + str(known)

    vcf_output = snakemake.output.get("vcf", "")
    if vcf_output:
        output = " --output " + str(vcf_output)

    gvcf_output = snakemake.output.get("gvcf", "")
    if gvcf_output:
        output = " --emit-ref-confidence GVCF " + " --output " + str(gvcf_output)

    if (vcf_output and gvcf_output) or (not gvcf_output and not vcf_output):
        if vcf_output and gvcf_output:
            raise ValueError(
                "please set vcf or gvcf as output, not both! It's not supported by gatk"
            )
        else:
            raise ValueError("please set one of vcf or gvcf as output (not both)!")

    bam_output = snakemake.output.get("bam", "")
    if bam_output:
        bam_output = " --bam-output " + str(bam_output)

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

    with tempfile.TemporaryDirectory() as tmpdir:
        shell(
            "gatk --java-options '{java_opts}' HaplotypeCaller"
            " --native-pair-hmm-threads {snakemake.threads}"
            " {bams}"
            " --reference {snakemake.input.ref}"
            " {intervals}"
            " {known}"
            " {extra}"
            " --tmp-dir {tmpdir}"
            " {output}"
            " {bam_output}"
            " {log}"
        )


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