.. _`bio/bcftools/filter`:

BCFTOOLS FILTER
===============


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

filter vcf/bcf file.

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

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule bcf_filter_sample:
        input:
            "{prefix}.bcf",  # input bcf/vcf needs to be first input
            samples="samples.txt",  # other inputs, e.g. sample files, are optional
        output:
            "{prefix}.filter_sample.vcf",
        log:
            "log/{prefix}.filter_sample.vcf.log",
        params:
            filter=lambda w, input: f"--exclude 'GT[@{input.samples}]=\"0/1\"'",
            extra="",
        wrapper:
            "v3.0.1/bio/bcftools/filter"


    rule bcf_filter_o_vcf:
        input:
            "{prefix}.bcf",
        output:
            "{prefix}.filter.vcf",
        log:
            "log/{prefix}.filter.vcf.log",
        params:
            filter="-i 'QUAL > 5'",
            extra="",
        wrapper:
            "v3.0.1/bio/bcftools/filter"


    rule bcf_filter_o_vcf_gz:
        input:
            "{prefix}.bcf",
        output:
            "{prefix}.filter.vcf.gz",
        log:
            "log/{prefix}.filter.vcf.gz.log",
        params:
            filter="-i 'QUAL > 5'",
            extra="",
        wrapper:
            "v3.0.1/bio/bcftools/filter"


    rule bcf_filter_o_bcf:
        input:
            "{prefix}.bcf",
        output:
            "{prefix}.filter.bcf",
        log:
            "log/{prefix}.filter.bcf.log",
        params:
            filter="-i 'QUAL > 5'",
            extra="",
        wrapper:
            "v3.0.1/bio/bcftools/filter"


    rule bcf_filter_o_uncompressed_bcf:
        input:
            "{prefix}.bcf",
        output:
            "{prefix}.filter.uncompressed.bcf",
        log:
            "log/{prefix}.filter.uncompressed.bcf.log",
        params:
            uncompressed_bcf=True,
            filter="-i 'QUAL > 5'",
            extra="",
        wrapper:
            "v3.0.1/bio/bcftools/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.


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``

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

* VCF/BCF file

**Output:**

* Filtered VCF/BCF file




Authors
-------

* Patrik Smeds
* Nikos Tsardakas Renhuldt
* Filipe G. Vieira


Code
----

.. code-block:: python

    __author__ = "Patrik Smeds"
    __copyright__ = "Copyright 2021, Patrik Smeds"
    __email__ = "patrik.smeds@scilifelab.uu.se"
    __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_samples=False, parse_memory=False
    )
    extra = snakemake.params.get("extra", "")
    log = snakemake.log_fmt_shell(stdout=False, stderr=True)
    filter = snakemake.params.get("filter", "")


    if len(snakemake.output) > 1:
        raise Exception("Only one output file expected, got: " + str(len(snakemake.output)))


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


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