.. _`bio/bcftools/view`:

BCFTOOLS VIEW
=============


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

View vcf/bcf file in a different format.

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

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule bcf_view_sample_file:
        input:
            "{prefix}.bcf",  # input bcf/vcf needs to be first input
            index="{prefix}.bcf.csi",  # other inputs are optional
            samples="samples.txt",
        output:
            "{prefix}.view_sample.vcf",
        log:
            "log/{prefix}.view_sample.vcf.log",
        params:
            # optional extra parameters
            extra=lambda w, input: f"-S {input.samples}",
        wrapper:
            "v4.6.0-24-g250dd3e/bio/bcftools/view"


    rule bcf_view_o_vcf:
        input:
            "{prefix}.bcf",
        output:
            "{prefix}.view.vcf",
        log:
            "log/{prefix}.view.vcf.log",
        params:
            extra="",
        wrapper:
            "v4.6.0-24-g250dd3e/bio/bcftools/view"


    rule bcf_view_o_vcf_gz:
        input:
            "{prefix}.bcf",
        output:
            "{prefix}.view.vcf.gz",
        log:
            "log/{prefix}.view.vcf.gz.log",
        params:
            extra="",
        wrapper:
            "v4.6.0-24-g250dd3e/bio/bcftools/view"


    rule bcf_view_o_bcf:
        input:
            "{prefix}.bcf",
        output:
            "{prefix}.view.bcf",
        log:
            "log/{prefix}.view.bcf.log",
        params:
            extra="",
        wrapper:
            "v4.6.0-24-g250dd3e/bio/bcftools/view"


    rule bcf_view_o_uncompressed_bcf:
        input:
            "{prefix}.bcf",
        output:
            "{prefix}.view.uncompressed.bcf",
        log:
            "log/{prefix}.view.uncompressed.bcf.log",
        params:
            uncompressed_bcf=True,
            extra="",
        wrapper:
            "v4.6.0-24-g250dd3e/bio/bcftools/view"

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``

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

* VCF/BCF file

**Output:**

* Filtered VCF/BCF file




Authors
-------

* Johannes Köster
* Nikos Tsardakas Renhuldt
* 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)

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


.. |nl| raw:: html

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