.. _`bio/bcftools/call`:

BCFTOOLS CALL
=============


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

Call variants with `bcftools call`.

**URL**: http://www.htslib.org/doc/bcftools.html#call

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule bcftools_call:
        input:
            pileup="{sample}.pileup.bcf",
        output:
            calls="{sample}.calls.bcf",
        params:
            uncompressed_bcf=False,
            caller="-m",  # valid options include -c/--consensus-caller or -m/--multiallelic-caller
            extra="--ploidy 1 --prior 0.001",
        log:
            "logs/bcftools_call/{sample}.log",
        wrapper:
            "v3.0.1/bio/bcftools/call"

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 `uncompressed_bcf` param allows to specify that a BCF output should be uncompressed (ignored otherwise).
* The `extra` param allows for additional program arguments (not `--threads`, `-o/--output`, or `-O/--output-type`).


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

* ``bcftools=1.18``
* ``snakemake-wrapper-utils=0.6.2``




Authors
-------

* Johannes Köster
* Michael Hall
* Filipe G. Vieira


Code
----

.. code-block:: python

    __author__ = "Johannes Köster"
    __copyright__ = "Copyright 2016, Johannes Köster"
    __email__ = "koester@jimmy.harvard.edu"
    __license__ = "MIT"


    from snakemake.shell import shell
    from snakemake_wrapper_utils.bcftools import get_bcftools_opts


    bcftools_opts = get_bcftools_opts(snakemake, parse_ref=False, parse_memory=False)
    extra = snakemake.params.get("extra", "")
    log = snakemake.log_fmt_shell(stdout=True, stderr=True)


    class CallerOptionError(Exception):
        pass


    valid_caller_opts = {"-c", "--consensus-caller", "-m", "--multiallelic-caller"}

    caller_opt = snakemake.params.get("caller", "")
    if caller_opt.strip() not in valid_caller_opts:
        raise CallerOptionError(
            "bcftools call expects either -m/--multiallelic-caller or "
            "-c/--consensus-caller as caller option."
        )


    shell(
        "bcftools call"
        " {bcftools_opts}"
        " {caller_opt}"
        " {extra}"
        " {snakemake.input[0]}"
        " {log}"
    )


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