.. _`bio/bcftools/merge`:

BCFTOOLS MERGE
==============


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

Merge vcf/bcf files with bcftools.

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

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule bcftools_merge:
        input:
            calls=["a.bcf", "b.bcf"],
            idx=["a.bcf.csi", "b.bcf.csi"],
        output:
            "all.bcf",
        log:
            "all.log",
        params:
            uncompressed_bcf=False,
            extra="",  # optional parameters for bcftools concat (except -o)
        wrapper:
            "v4.6.0-24-g250dd3e/bio/bcftools/merge"

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=1.21``
* ``snakemake-wrapper-utils=0.6.2``




Authors
-------

* Patrik Smeds
* Filipe G. Vieira


Code
----

.. code-block:: python

    __author__ = "Patrik Smeds"
    __copyright__ = "Copyright 2018, Patrik Smeds"
    __email__ = "patrik.smeds@gmail.com"
    __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)

    shell("bcftools merge {bcftools_opts} {extra} {snakemake.input.calls} {log}")


.. |nl| raw:: html

   <br>