.. _`bio/vcftools/filter`:

VCFTOOLS FILTER
===============


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

Filter vcf files using vcftools


Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule filter_vcf:
        input:
            "{sample}.vcf"
        output:
            "{sample}.filtered.vcf"
        params:
            extra="--chr 1 --recode-INFO-all"
        wrapper:
            "v3.0.4/bio/vcftools/filter"

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.


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

* ``vcftools=0.1.16``




Authors
-------

* Patrik Smeds


Code
----

.. code-block:: python

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


    from snakemake.shell import shell

    input_flag = "--vcf"
    if snakemake.input[0].endswith(".gz"):
        input_flag = "--gzvcf"

    output = " > " + snakemake.output[0]
    if output.endswith(".gz"):
        output = " | gzip" + output

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

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

    shell(
        "vcftools "
        "{input_flag} "
        "{snakemake.input} "
        "{extra} "
        "--recode "
        "--stdout "
        "{output} "
        "{log}"
    )


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