.. _`bio/bcftools/norm`:

BCFTOOLS NORM
=============


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

Left-align and normalize indels, check if REF alleles match the reference, split multiallelic sites into multiple rows; recover multiallelics from multiple rows.

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

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule norm_vcf:
        input:
            "{prefix}.bcf",
            #ref="genome.fasta"  # optional reference (will be translated into the -f option)
        output:
            "{prefix}.norm.vcf",  # can also be .bcf, corresponding --output-type parameter is inferred automatically
        log:
            "{prefix}.norm.log",
        params:
            extra="--rm-dup none",  # optional
            #uncompressed_bcf=False,
        wrapper:
            "v3.0.1/bio/bcftools/norm"

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`, `-f/--fasta-ref`, `-o/--output`, or `-O/--output-type`).


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

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




Authors
-------

* Dayne Filer
* Filipe G. Vieira


Code
----

.. code-block:: python

    __author__ = "Dayne Filer"
    __copyright__ = "Copyright 2019, Dayne Filer"
    __email__ = "dayne.filer@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_memory=False)
    extra = snakemake.params.get("extra", "")
    log = snakemake.log_fmt_shell(stdout=True, stderr=True)


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


.. |nl| raw:: html

   <br>